diff --git a/applications/compute_loop_velocity.py b/applications/compute_loop_velocity.py
new file mode 100644
index 00000000..f30968b2
--- /dev/null
+++ b/applications/compute_loop_velocity.py
@@ -0,0 +1,87 @@
+import argparse
+import csv
+import json
+import os
+
+from bird import logger
+from bird.postprocess.post_quantities import (
+    build_loop_direction_field,
+    build_loop_direction_field_from_path,
+    compute_loop_velocity,
+    propose_loop_boxes_block_rect,
+)
+from bird.utilities.ofio import get_case_times, read_cell_centers
+
+
+def build_direction_field(args, cell_centers):
+    """Loop-direction field from the box, path, or block-rect proposer source."""
+    if args.boxes is not None:
+        with open(args.boxes) as f:
+            boxes = json.load(f)
+        return build_loop_direction_field(cell_centers, boxes)
+    if args.path is not None:
+        with open(args.path) as f:
+            spec = json.load(f)
+        return build_loop_direction_field_from_path(
+            cell_centers, spec["points"], spec["max_dist"]
+        )
+    with open(args.mesh) as f:
+        geometry = json.load(f)["Geometry"]
+    boxes = propose_loop_boxes_block_rect(geometry, rescale=args.rescale)
+    return build_loop_direction_field(cell_centers, boxes)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Loop (circulation) velocity")
+    parser.add_argument(
+        "-c", "--case", type=str, default=".", help="case folder"
+    )
+    source = parser.add_mutually_exclusive_group(required=True)
+    source.add_argument(
+        "-b", "--boxes", type=str, help="JSON list of {min, max, direction}"
+    )
+    source.add_argument(
+        "-p",
+        "--path",
+        type=str,
+        help='JSON {"points": [[x,y,z], ...], "max_dist": float}',
+    )
+    source.add_argument(
+        "-m", "--mesh", type=str, help="mesh.json for the block-rect proposer"
+    )
+    parser.add_argument(
+        "-r",
+        "--rescale",
+        type=float,
+        default=None,
+        help="rescale factor for the proposer (default 1.0)",
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=str,
+        default=None,
+        help="output CSV (default <case>/Uliq_loop.csv)",
+    )
+    args = parser.parse_args()
+
+    cell_centers, _ = read_cell_centers(args.case)
+    direction_field = build_direction_field(args, cell_centers)
+
+    time_values, time_names = get_case_times(args.case, remove_zero=True)
+    output = args.output or os.path.join(args.case, "Uliq_loop.csv")
+    with open(output, "w", newline="") as f:
+        writer = csv.writer(f)
+        writer.writerow(["time", "U_loop"])
+        for time_value, time_name in zip(time_values, time_names):
+            # fresh cache per time (the caller must reset it)
+            u_loop, _ = compute_loop_velocity(
+                args.case, time_name, direction_field, field_dict={}
+            )
+            writer.writerow([time_value, u_loop])
+            logger.info(f"t={time_value:.4g}: U_loop={u_loop:.6g}")
+    logger.info(f"Wrote {output}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/bird/postprocess/post_quantities/__init__.py b/bird/postprocess/post_quantities/__init__.py
index 23ecfc38..7e8be921 100644
--- a/bird/postprocess/post_quantities/__init__.py
+++ b/bird/postprocess/post_quantities/__init__.py
@@ -5,17 +5,59 @@
     _get_ind_slice,
     _weighted_average,
 )
-from .kla import compute_fitted_kla, compute_instantaneous_kla
-from .phase import compute_ave_bubble_diam, compute_gas_holdup
+from .dimensionless import (
+    compute_froude_number,
+    compute_sherwood_number,
+    compute_weber_number,
+    froude,
+    sherwood,
+    weber,
+)
+from .kla import (
+    compute_fitted_kl,
+    compute_fitted_kla,
+    compute_instantaneous_kl,
+    compute_instantaneous_kla,
+)
+from .loop_velocity import (
+    build_loop_direction_field,
+    build_loop_direction_field_from_path,
+    compute_loop_velocity,
+    propose_loop_boxes_block_rect,
+)
+from .phase import (
+    compute_ave_bubble_diam,
+    compute_ave_liquid_density,
+    compute_ave_liquid_velocity,
+    compute_gas_holdup,
+    interfacial_area,
+)
 from .species import compute_ave_conc_liq, compute_ave_y_liq
 from .superficial_velocity import compute_superficial_gas_velocity
+from .transport import compute_turbulent_diffusivity
 
 __all__ = [
+    "build_loop_direction_field",
+    "build_loop_direction_field_from_path",
     "compute_ave_bubble_diam",
     "compute_ave_conc_liq",
+    "compute_ave_liquid_density",
+    "compute_ave_liquid_velocity",
     "compute_ave_y_liq",
+    "compute_fitted_kl",
     "compute_fitted_kla",
+    "compute_froude_number",
     "compute_gas_holdup",
+    "compute_instantaneous_kl",
     "compute_instantaneous_kla",
+    "compute_loop_velocity",
+    "compute_sherwood_number",
     "compute_superficial_gas_velocity",
+    "compute_turbulent_diffusivity",
+    "compute_weber_number",
+    "froude",
+    "interfacial_area",
+    "propose_loop_boxes_block_rect",
+    "sherwood",
+    "weber",
 ]
diff --git a/bird/postprocess/post_quantities/dimensionless.py b/bird/postprocess/post_quantities/dimensionless.py
new file mode 100644
index 00000000..9b3730c5
--- /dev/null
+++ b/bird/postprocess/post_quantities/dimensionless.py
@@ -0,0 +1,235 @@
+import numpy as np
+
+from bird.utilities.ofio import (
+    read_global_vars,
+    read_gravity,
+    read_surface_tension,
+)
+
+from .kla import compute_instantaneous_kl
+from .phase import compute_ave_liquid_density, compute_ave_liquid_velocity
+
+
+def froude(velocity: float, length: float, gravity: float = 9.81) -> float:
+    r"""Froude number :math:`Fr = U / \sqrt{g\,L}`.
+
+    Parameters
+    ----------
+    velocity: float
+        Characteristic velocity :math:`U`, in :math:`m.s^{-1}`
+    length: float
+        Characteristic length :math:`L`, in :math:`m`
+    gravity: float
+        Gravitational acceleration :math:`g`, in :math:`m.s^{-2}`
+
+    Returns
+    ----------
+    froude_number: float
+        Froude number (dimensionless)
+    """
+    return velocity / np.sqrt(gravity * length)
+
+
+def weber(
+    density: float, velocity: float, length: float, surface_tension: float
+) -> float:
+    r"""Weber number :math:`We = \rho\,U^2\,L / \sigma`.
+
+    Parameters
+    ----------
+    density: float
+        Fluid density :math:`\rho`, in :math:`kg.m^{-3}`
+    velocity: float
+        Characteristic velocity :math:`U`, in :math:`m.s^{-1}`
+    length: float
+        Characteristic length :math:`L`, in :math:`m`
+    surface_tension: float
+        Surface tension :math:`\sigma`, in :math:`N.m^{-1}`
+
+    Returns
+    ----------
+    weber_number: float
+        Weber number (dimensionless)
+    """
+    return density * velocity**2 * length / surface_tension
+
+
+def sherwood(kl: float, length: float, diffusivity: float) -> float:
+    r"""Sherwood number :math:`Sh = k_L\,L / D`.
+
+    Parameters
+    ----------
+    kl: float
+        Mass-transfer coefficient :math:`k_L`, in :math:`m.s^{-1}`
+    length: float
+        Characteristic length :math:`L`, in :math:`m`
+    diffusivity: float
+        Mass diffusivity :math:`D`, in :math:`m^2.s^{-1}`
+
+    Returns
+    ----------
+    sherwood_number: float
+        Sherwood number (dimensionless)
+    """
+    return kl * length / diffusivity
+
+
+def compute_froude_number(
+    case_folder: str,
+    time_folder: str,
+    length: float,
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Froude number from the liquid-averaged velocity and a given length.
+
+    :math:`Fr = U / \sqrt{g L}` with :math:`U` the liquid-volume-averaged
+    :math:`|U_{\rm liq}|` at ``time_folder``, :math:`g` from ``constant/g``, and
+    :math:`L` the passed length.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    length: float
+        Characteristic length :math:`L`, in :math:`m`
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    froude_number: float
+        Froude number (dimensionless)
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+    velocity, field_dict = compute_ave_liquid_velocity(
+        case_folder, time_folder, n_cells, volume_time, field_dict
+    )
+    gravity = read_gravity(case_folder)
+    return froude(velocity, length, gravity=gravity), field_dict
+
+
+def compute_weber_number(
+    case_folder: str,
+    time_folder: str,
+    length: float,
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Weber number from the liquid-averaged velocity/density and a given length.
+
+    :math:`We = \rho U^2 L / \sigma` with :math:`U` and :math:`\rho` the
+    liquid-volume-averaged velocity magnitude and density at ``time_folder``,
+    :math:`\sigma` from ``constant/phaseProperties``, and :math:`L` the passed
+    length.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    length: float
+        Characteristic length :math:`L`, in :math:`m`
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    weber_number: float
+        Weber number (dimensionless)
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+    velocity, field_dict = compute_ave_liquid_velocity(
+        case_folder, time_folder, n_cells, volume_time, field_dict
+    )
+    density, field_dict = compute_ave_liquid_density(
+        case_folder, time_folder, n_cells, volume_time, field_dict
+    )
+    surface_tension = read_surface_tension(case_folder)
+    return weber(density, velocity, length, surface_tension), field_dict
+
+
+def compute_sherwood_number(
+    case_folder: str,
+    time_folder: str,
+    length: float,
+    species_name: str,
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Sherwood number for one species from the instantaneous kL.
+
+    :math:`Sh = k_L L / D` with :math:`k_L` from
+    :func:`compute_instantaneous_kl` at ``time_folder`` and the molecular
+    diffusivity :math:`D` read as ``D_<species>`` from globalVars (the standard
+    Sherwood definition; the turbulent contribution is deliberately excluded).
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    length: float
+        Characteristic length :math:`L`, in :math:`m`
+    species_name: str
+        Species for which to compute kL and use D_<species>
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    sherwood_number: float
+        Sherwood number (dimensionless)
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+    kl_spec, _, field_dict = compute_instantaneous_kl(
+        case_folder,
+        time_folder,
+        species_name,
+        n_cells=n_cells,
+        volume_time=volume_time,
+        field_dict=field_dict,
+    )
+    diffusivity = float(
+        read_global_vars(case_folder=case_folder, cross_ref=True)[
+            f"D_{species_name}"
+        ]
+    )
+    # kL from compute_instantaneous_kl is in m/h, but D is in m2/s, so kL must
+    # be converted back to m/s for Sh to come out dimensionless.
+    kl_m_per_s = kl_spec[species_name] / 3600
+    return sherwood(kl_m_per_s, length, diffusivity), field_dict
diff --git a/bird/postprocess/post_quantities/kla.py b/bird/postprocess/post_quantities/kla.py
index c60a666b..82082f03 100644
--- a/bird/postprocess/post_quantities/kla.py
+++ b/bird/postprocess/post_quantities/kla.py
@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 
 from bird import logger
@@ -16,9 +14,194 @@
 
 from ..kla_utils import compute_kla
 from ._cell_filter import _field_filter, _get_ind_liq, _weighted_average
+from .phase import (
+    _read_liquid_density_field,
+    compute_ave_bubble_diam,
+    compute_gas_holdup,
+    interfacial_area,
+)
 from .species import compute_ave_conc_liq
 
 
+def _instantaneous_kl_field(
+    case_folder: str,
+    time_folder: str,
+    species_names: str | list[str],
+    n_cells: int | None = None,
+    field_dict: dict | None = None,
+) -> tuple[dict, dict]:
+    """Per-cell mass-transfer coefficient kL over the liquid, per species."""
+    if field_dict is None:
+        field_dict = {}
+    if isinstance(species_names, str):
+        species_names = [species_names]
+
+    kwargs = {
+        "case_folder": case_folder,
+        "time_folder": time_folder,
+        "n_cells": n_cells,
+    }
+    globalVars = read_global_vars(case_folder=case_folder, cross_ref=True)
+    ind_liq, field_dict = _get_ind_liq(field_dict=field_dict, **kwargs)
+
+    rho_liq, field_dict = _read_liquid_density_field(
+        case_folder, time_folder, n_cells, field_dict
+    )
+    U_gas, field_dict = read_field(
+        field_name="U.gas", field_dict=field_dict, **kwargs
+    )
+    U_liq, field_dict = read_field(
+        field_name="U.liquid", field_dict=field_dict, **kwargs
+    )
+    d_gas, field_dict = read_bubble_diameter(field_dict=field_dict, **kwargs)
+    mu_liq, field_dict = read_mu_liquid(field_dict=field_dict, **kwargs)
+
+    rho_liq = _field_filter(rho_liq, ind=ind_liq, field_type="scalar")
+    U_gas = _field_filter(U_gas, ind=ind_liq, field_type="vector")
+    U_liq = _field_filter(U_liq, ind=ind_liq, field_type="vector")
+    d_gas = _field_filter(d_gas, ind=ind_liq, field_type="scalar")
+    mu_liq = _field_filter(mu_liq, ind=ind_liq, field_type="scalar")
+
+    # Magnitude of the slip velocity. Using the last axis keeps this valid
+    # whether the velocities are uniform, shape (3,), or per cell, shape (N,3)
+    mag_U_diff = np.linalg.norm(U_gas - U_liq, axis=-1)
+    Re = rho_liq * mag_U_diff * d_gas / mu_liq
+
+    kl_spec_field = {}
+    for species_name in species_names:
+        if not f"D_{species_name}" in globalVars:
+            err_msg = f"D_{species_name} was not found in globalVars."
+            err_msg += f'\nIf you add it, it should be looking like #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_{species_name},0.6)";'
+            raise KeyError(err_msg)
+        kl_spec_field[species_name] = (
+            (2 / np.pi**0.5)
+            * 3600
+            * (Re**0.5)
+            * (((mu_liq / rho_liq) / globalVars[f"D_{species_name}"]) ** 0.5)
+            * (globalVars[f"D_{species_name}"] / d_gas)
+        )
+    return kl_spec_field, field_dict
+
+
+def _instantaneous_a_field(
+    case_folder: str,
+    time_folder: str,
+    n_cells: int | None = None,
+    field_dict: dict | None = None,
+) -> tuple[np.ndarray | float, dict]:
+    """Per-cell interfacial area a = 6 alpha_gas / d over the liquid."""
+    if field_dict is None:
+        field_dict = {}
+    kwargs = {
+        "case_folder": case_folder,
+        "time_folder": time_folder,
+        "n_cells": n_cells,
+    }
+    ind_liq, field_dict = _get_ind_liq(field_dict=field_dict, **kwargs)
+    alpha_gas, field_dict = read_field(
+        field_name="alpha.gas", field_dict=field_dict, **kwargs
+    )
+    d_gas, field_dict = read_bubble_diameter(field_dict=field_dict, **kwargs)
+    alpha_gas = _field_filter(alpha_gas, ind=ind_liq, field_type="scalar")
+    d_gas = _field_filter(d_gas, ind=ind_liq, field_type="scalar")
+    return (6.0 / d_gas) * alpha_gas, field_dict
+
+
+def _instantaneous_kla_field(
+    case_folder: str,
+    time_folder: str,
+    species_names: str | list[str],
+    n_cells: int | None = None,
+    field_dict: dict | None = None,
+) -> tuple[dict, dict]:
+    """Per-cell kLa = kL * a over the liquid, per species."""
+    if field_dict is None:
+        field_dict = {}
+    if isinstance(species_names, str):
+        species_names = [species_names]
+    kl_spec_field, field_dict = _instantaneous_kl_field(
+        case_folder, time_folder, species_names, n_cells, field_dict
+    )
+    a_field, field_dict = _instantaneous_a_field(
+        case_folder, time_folder, n_cells, field_dict
+    )
+    kla_spec_field = {
+        species_name: kl_spec_field[species_name] * a_field
+        for species_name in species_names
+    }
+    return kla_spec_field, field_dict
+
+
+def _instantaneous_cstar(
+    case_folder: str,
+    time_folder: str,
+    species_names: str | list[str],
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[dict, dict]:
+    """Volume-averaged saturation concentration C* over the liquid, per species."""
+    if field_dict is None:
+        field_dict = {}
+    if isinstance(species_names, str):
+        species_names = [species_names]
+    kwargs = {
+        "case_folder": case_folder,
+        "time_folder": time_folder,
+        "n_cells": n_cells,
+    }
+    kwargs_vol = {
+        "case_folder": case_folder,
+        "time_folder": volume_time,
+        "n_cells": n_cells,
+    }
+    globalVars = read_global_vars(case_folder=case_folder, cross_ref=True)
+    mw_species = {}
+    for species_name in species_names:
+        if not f"He_{species_name}" in globalVars:
+            err_msg = f"He_{species_name} was not found in globalVars."
+            err_msg += f'\nIf you add it, it should be looking like #calc "$H_{species_name}_298 * exp($DH_{species_name} *(1. / $T0 - 1./298.15))";'
+            raise KeyError(err_msg)
+        mw_species[species_name] = species_name_to_mw(
+            case_folder=case_folder, species_name=species_name
+        )
+    ind_liq, field_dict = _get_ind_liq(field_dict=field_dict, **kwargs)
+    alpha_gas, field_dict = read_field(
+        field_name="alpha.gas", field_dict=field_dict, **kwargs
+    )
+    rho_gas, field_dict = read_field(
+        field_name="thermo:rho.gas", field_dict=field_dict, **kwargs
+    )
+    species_gas = {}
+    for species_name in species_names:
+        species_gas[species_name], field_dict = read_field(
+            field_name=f"{species_name}.gas", field_dict=field_dict, **kwargs
+        )
+    alpha_gas = _field_filter(alpha_gas, ind=ind_liq, field_type="scalar")
+    alpha_liq = 1 - alpha_gas
+    rho_gas = _field_filter(rho_gas, ind=ind_liq, field_type="scalar")
+    for species_name in species_names:
+        species_gas[species_name] = _field_filter(
+            species_gas[species_name], ind=ind_liq, field_type="scalar"
+        )
+    cell_volume, field_dict = read_cell_volumes(
+        field_dict=field_dict, **kwargs_vol
+    )
+    cell_volume = _field_filter(cell_volume, ind=ind_liq, field_type="scalar")
+
+    cstar_spec = {}
+    for species_name in species_names:
+        cstar_field = (
+            rho_gas
+            * species_gas[species_name]
+            * globalVars[f"He_{species_name}"]
+        ) / mw_species[species_name]
+        cstar_spec[species_name] = _weighted_average(
+            cstar_field, cell_volume * alpha_liq
+        )
+    return cstar_spec, field_dict
+
+
 def compute_instantaneous_kla(
     case_folder: str,
     time_folder: str,
@@ -98,11 +281,11 @@ def compute_instantaneous_kla(
     Returns
     ----------
     kla_spec: dict
-        Instantaneous volume averaged kLa for each species
+        Instantaneous volume averaged kLa for each species, in :math:`h^{-1}`
         Keys are species names
         Values are the kLa values
     cstar_spec: dict
-        Instantaneous volume averaged cstar for each species
+        Instantaneous volume averaged cstar for each species, in :math:`mol.m^{-3}`
         Keys are species names
         Values are the cstar values
     field_dict : dict
@@ -110,11 +293,9 @@ def compute_instantaneous_kla(
     """
     if field_dict is None:
         field_dict = {}
-
     if isinstance(species_names, str):
         species_names = [species_names]
 
-    # Read relevant fields
     kwargs = {
         "case_folder": case_folder,
         "time_folder": time_folder,
@@ -126,118 +307,137 @@ def compute_instantaneous_kla(
         "n_cells": n_cells,
     }
 
-    # Read globarVars into a python dict
-    # Replace all the #calc entries with their numeral values
-    globalVars = read_global_vars(case_folder=case_folder, cross_ref=True)
-
-    # Check that global vars has the values we want and provide a useful error message otherwise
-    mw_species = {}
-    for species_name in species_names:
-        if not f"He_{species_name}" in globalVars:
-            err_msg = f"He_{species_name} was not found in globalVars."
-            err_msg += f'\nIf you add it, it should be looking like #calc "$H_{species_name}_298 * exp($DH_{species_name} *(1. / $T0 - 1./298.15))";'
-            raise KeyError(err_msg)
-        if not f"D_{species_name}" in globalVars:
-            err_msg = f"D_{species_name} was not found in globalVars."
-            err_msg += f'\nIf you add it, it should be looking like #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_{species_name},0.6)";'
-            raise KeyError(err_msg)
-        mw_species[species_name] = species_name_to_mw(
-            case_folder=case_folder, species_name=species_name
-        )
+    kla_spec_field, field_dict = _instantaneous_kla_field(
+        case_folder, time_folder, species_names, n_cells, field_dict
+    )
 
-    # Get liquid domain
+    # Volume average over the liquid
     ind_liq, field_dict = _get_ind_liq(field_dict=field_dict, **kwargs)
-
-    # Read all the fields
-    alpha_gas, field_dict = read_field(
-        field_name="alpha.gas", field_dict=field_dict, **kwargs
+    cell_volume, field_dict = read_cell_volumes(
+        field_dict=field_dict, **kwargs_vol
     )
-    try:
-        rho_liq, field_dict = read_field(
-            field_name="thermo:rho.liquid", field_dict=field_dict, **kwargs
-        )
-    except FileNotFoundError:
-        abs_time_path = os.path.join(case_folder, time_folder)
-        logger.warning(
-            f"thermo:rho.liquid not found in {abs_time_path}, assuming it is 1000kg/m3"
+    cell_volume = _field_filter(cell_volume, ind=ind_liq, field_type="scalar")
+    kla_spec = {
+        species_name: _weighted_average(
+            kla_spec_field[species_name], cell_volume
         )
-        rho_liq = 1000.0
-        field_dict["rho_liq"] = rho_liq
-
-    rho_gas, field_dict = read_field(
-        field_name="thermo:rho.gas", field_dict=field_dict, **kwargs
-    )
-    U_gas, field_dict = read_field(
-        field_name="U.gas", field_dict=field_dict, **kwargs
-    )
-    U_liq, field_dict = read_field(
-        field_name="U.liquid", field_dict=field_dict, **kwargs
+        for species_name in species_names
+    }
+    cstar_spec, field_dict = _instantaneous_cstar(
+        case_folder,
+        time_folder,
+        species_names,
+        n_cells,
+        volume_time,
+        field_dict,
     )
-    d_gas, field_dict = read_bubble_diameter(field_dict=field_dict, **kwargs)
+    return kla_spec, cstar_spec, field_dict
 
-    mu_liq, field_dict = read_mu_liquid(field_dict=field_dict, **kwargs)
-    species_gas = {}
-    for species_name in species_names:
-        species_gas[species_name], field_dict = read_field(
-            field_name=f"{species_name}.gas", field_dict=field_dict, **kwargs
-        )
 
-    # Only compute over the liquid
-    alpha_gas = _field_filter(alpha_gas, ind=ind_liq, field_type="scalar")
-    alpha_liq = 1 - alpha_gas
-    rho_liq = _field_filter(rho_liq, ind=ind_liq, field_type="scalar")
-    rho_gas = _field_filter(rho_gas, ind=ind_liq, field_type="scalar")
-    U_gas = _field_filter(U_gas, ind=ind_liq, field_type="vector")
-    U_liq = _field_filter(U_liq, ind=ind_liq, field_type="vector")
-    d_gas = _field_filter(d_gas, ind=ind_liq, field_type="scalar")
-    mu_liq = _field_filter(mu_liq, ind=ind_liq, field_type="scalar")
-    for species_name in species_names:
-        species_gas[species_name] = _field_filter(
-            species_gas[species_name], ind=ind_liq, field_type="scalar"
-        )
+def compute_instantaneous_kl(
+    case_folder: str,
+    time_folder: str,
+    species_names: str | list[str],
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[dict, dict]:
+    r"""
+    Calculate the mass-transfer coefficient (:math:`kL_{\rm spec}`) and saturation concentration (:math:`C^*_{\rm spec}`) for a list of species from instantaneous data (rather than doing a fit over time).
 
-    # Magnitude of the slip velocity. Using the last axis keeps this valid
-    # whether the velocities are uniform, shape (3,), or per cell, shape (N,3)
-    mag_U_diff = np.linalg.norm(U_gas - U_liq, axis=-1)
+    :math:`kL_{\rm spec}` is the penetration-theory coefficient that
+    :func:`compute_instantaneous_kla` multiplies by the interfacial area
+    :math:`a = 6 \alpha_{\rm gas} / d_{\rm gas}` to form :math:`kLa_{\rm spec}`
+    (i.e. :math:`kLa_{\rm spec} = kL_{\rm spec}\, a`), volume averaged over the liquid.
 
-    # Compute kLa
-    Re = rho_liq * mag_U_diff * d_gas / mu_liq
-    kla_spec_field = {}
-    for species_name in species_names:
-        kla_spec_field[species_name] = (
-            (2 / np.pi**0.5)
-            * 3600
-            * (Re**0.5)
-            * (((mu_liq / rho_liq) / globalVars[f"D_{species_name}"]) ** 0.5)
-            * (globalVars[f"D_{species_name}"] / d_gas)
-            * (6.0 / d_gas)
-            * alpha_gas
-        )
-    cstar_spec_field = {}
-    for species_name in species_names:
-        cstar_spec_field[species_name] = (
-            rho_gas
-            * species_gas[species_name]
-            * globalVars[f"He_{species_name}"]
-        ) / mw_species[species_name]
+    .. math::
+
+       \frac{1}{V_{\rm liq, tot}} \int_{V_{\rm liq}} kL_{\rm spec} dV
+
+    .. math::
+
+       kL_{\rm spec} = 3600 \sqrt{\frac{4 D_{\rm spec} |u_{\rm slip}|}{\pi d_{\rm gas}}}
+
+    where:
+      - :math:`kL_{\rm spec}` is the mass transfer coefficient in :math:`m.h^{-1}`
+      - :math:`d_{\rm gas}` is the bubble diameter in :math:`m`. Either read from the time folder, or looked up from phaseProperties
+      - :math:`D_{\rm spec}` is the species molecular diffusivity in :math:`m^2.s^{-1}`. Read from globalVars
+      - :math:`|u_{\rm slip}|` is the magnitude of the slip velocity in :math:`m.s^{-1}`. Read from the time folder.
+      - :math:`V_{\rm liq}` is the volume of liquid in :math:`m^3`. Read from the time folder.
+
+    :math:`C^*_{\rm spec}` is computed as in :func:`compute_instantaneous_kla`.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of time folder to analyze
+    species_names: str | list[str]
+        List of species name for which to compute kL
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    kl_spec: dict
+        Instantaneous volume averaged kL for each species, in :math:`m.h^{-1}`
+        Keys are species names
+        Values are the kL values
+    cstar_spec: dict
+        Instantaneous volume averaged cstar for each species, in :math:`mol.m^{-3}`
+        Keys are species names
+        Values are the cstar values
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+    if isinstance(species_names, str):
+        species_names = [species_names]
+
+    kwargs = {
+        "case_folder": case_folder,
+        "time_folder": time_folder,
+        "n_cells": n_cells,
+    }
+    kwargs_vol = {
+        "case_folder": case_folder,
+        "time_folder": volume_time,
+        "n_cells": n_cells,
+    }
 
-    # Do volume average
+    kl_spec_field, field_dict = _instantaneous_kl_field(
+        case_folder, time_folder, species_names, n_cells, field_dict
+    )
+
+    # Volume average over the liquid
+    ind_liq, field_dict = _get_ind_liq(field_dict=field_dict, **kwargs)
     cell_volume, field_dict = read_cell_volumes(
         field_dict=field_dict, **kwargs_vol
     )
     cell_volume = _field_filter(cell_volume, ind=ind_liq, field_type="scalar")
-
-    kla_spec = {}
-    cstar_spec = {}
-    for species_name in species_names:
-        kla_spec[species_name] = _weighted_average(
-            kla_spec_field[species_name], cell_volume
+    kl_spec = {
+        species_name: _weighted_average(
+            kl_spec_field[species_name], cell_volume
         )
-        cstar_spec[species_name] = _weighted_average(
-            cstar_spec_field[species_name], cell_volume * alpha_liq
-        )
-
-    return kla_spec, cstar_spec, field_dict
+        for species_name in species_names
+    }
+    cstar_spec, field_dict = _instantaneous_cstar(
+        case_folder,
+        time_folder,
+        species_names,
+        n_cells,
+        volume_time,
+        field_dict,
+    )
+    return kl_spec, cstar_spec, field_dict
 
 
 def compute_fitted_kla(
@@ -291,11 +491,11 @@ def compute_fitted_kla(
     Returns
     ----------
     kla_spec: dict
-        Instantaneous volume averaged kLa for each species
+        Instantaneous volume averaged kLa for each species, in :math:`h^{-1}`
         Keys are species names
         Values are dictionaries with key 'mean' (mean kLa value) and 'std' (1 standard deviation for the kLa value)
     cstar_spec: dict
-        Instantaneous volume averaged cstar for each species
+        Instantaneous volume averaged cstar for each species, in :math:`mol.m^{-3}`
         Keys are species names
         Values are dictionaries with key 'mean' (mean cstar value) and 'std' (1 standard deviation for the cstar value)
     field_dict : dict
@@ -317,10 +517,6 @@ def compute_fitted_kla(
     # Get all the time folders
     time_float_sorted, time_str_sorted = get_case_times(case_folder)
 
-    # Read globarVars into a python dict
-    # Replace all the #calc entries with their numeral values
-    globalVars = read_global_vars(case_folder=case_folder, cross_ref=True)
-
     # Get Mw of the species
     mw_species = {}
     for species_name in species_names:
@@ -386,3 +582,83 @@ def compute_fitted_kla(
         }
 
     return kla_spec, cstar_spec, field_dict
+
+
+def compute_fitted_kl(
+    case_folder: str,
+    species_names: str | list[str],
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    num_warmup: int = 4000,
+    num_samples: int = 1000,
+    field_dict: dict | None = None,
+) -> tuple[dict, dict, dict]:
+    r"""Fitted mass-transfer coefficient :math:`kL = kLa / a`.
+
+    Same as :func:`compute_fitted_kla` but the fitted mean and std of each
+    species are divided by the interfacial area :math:`a = 6\,\epsilon / d`,
+    evaluated at the last time folder.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    species_names: str | list[str]
+        List of species name for which to compute kL
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    num_warmup: int
+        Number of MCMC samples in the warmup phase
+        Defaults to 4000
+    num_samples: int
+        Number of posterior MCMC samples generated
+        Defaults to 1000
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    kl_spec: dict
+        Fitted volume averaged kL for each species, in :math:`m.h^{-1}`
+        Keys are species names
+        Values are dictionaries with key 'mean' (mean kL value) and 'std' (1 standard deviation for the kL value)
+    cstar_spec: dict
+        Fitted volume averaged cstar for each species, in :math:`mol.m^{-3}`
+        Keys are species names
+        Values are dictionaries with key 'mean' (mean cstar value) and 'std' (1 standard deviation for the cstar value)
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+
+    kla_spec, cstar_spec, field_dict = compute_fitted_kla(
+        case_folder,
+        species_names,
+        n_cells=n_cells,
+        volume_time=volume_time,
+        num_warmup=num_warmup,
+        num_samples=num_samples,
+        field_dict=field_dict,
+    )
+    # interfacial area at the last time folder
+    _, time_str_sorted = get_case_times(case_folder)
+    last_time = time_str_sorted[-1]
+    area_cache: dict = {}
+    gas_holdup, area_cache = compute_gas_holdup(
+        case_folder, last_time, n_cells, volume_time, area_cache
+    )
+    bubble_diam, area_cache = compute_ave_bubble_diam(
+        case_folder, last_time, n_cells, volume_time, area_cache
+    )
+    area = interfacial_area(gas_holdup, bubble_diam)
+
+    kl_spec = {
+        species: {"mean": kla["mean"] / area, "std": kla["std"] / area}
+        for species, kla in kla_spec.items()
+    }
+    return kl_spec, cstar_spec, field_dict
diff --git a/bird/postprocess/post_quantities/loop_velocity.py b/bird/postprocess/post_quantities/loop_velocity.py
new file mode 100644
index 00000000..25a2b8b4
--- /dev/null
+++ b/bird/postprocess/post_quantities/loop_velocity.py
@@ -0,0 +1,303 @@
+import numpy as np
+
+from bird import logger
+from bird.meshing.block_rect_mesh import from_block_rect_to_seg
+from bird.utilities.ofio import read_cell_volumes, read_field
+
+from ._cell_filter import _weighted_average
+
+
+def _normalize(vector: np.ndarray) -> np.ndarray:
+    """Unit vector along ``vector`` (raises on a zero vector)."""
+    norm = np.linalg.norm(vector)
+    if norm == 0:
+        raise ValueError("Cannot normalize a zero-length direction vector")
+    return vector / norm
+
+
+def _report_coverage(covered: np.ndarray) -> None:
+    """Warn about the fraction of uncovered cells; list their ids in debug."""
+    n_cells = len(covered)
+    n_uncovered = int(np.count_nonzero(~covered))
+    if n_uncovered:
+        logger.warning(
+            f"{n_uncovered}/{n_cells} cells "
+            f"({100.0 * n_uncovered / n_cells:.2f}%) have no loop direction "
+            f"and are excluded from the loop velocity"
+        )
+        logger.debug(
+            f"Uncovered cell ids: {np.flatnonzero(~covered).tolist()}"
+        )
+
+
+def build_loop_direction_field(
+    cell_centers: np.ndarray, boxes: list[dict]
+) -> np.ndarray:
+    """Per-cell loop-direction field from labelled axis-aligned boxes.
+
+    Each cell inherits the (unit) direction of the box that contains its centre.
+    Cells in no box keep ``NaN`` (excluded from the average); a cell in more than
+    one box is ambiguous and raises.
+
+    Parameters
+    ----------
+    cell_centers: np.ndarray
+        Cell centres, shape ``(N, 3)``
+    boxes: list[dict]
+        List of ``{"min": [x, y, z], "max": [x, y, z], "direction": [dx, dy, dz]}``;
+        ``direction`` is normalized internally
+
+    Returns
+    ----------
+    direction_field: np.ndarray
+        Direction field, shape ``(N, 3)``, ``NaN`` where uncovered
+    """
+    cell_centers = np.asarray(cell_centers, dtype=float)
+    n_cells = len(cell_centers)
+    direction_field = np.full((n_cells, 3), np.nan)
+    coverage_count = np.zeros(n_cells, dtype=int)
+
+    for box in boxes:
+        box_min = np.asarray(box["min"], dtype=float)
+        box_max = np.asarray(box["max"], dtype=float)
+        direction = _normalize(np.asarray(box["direction"], dtype=float))
+        inside = np.all(
+            (cell_centers >= box_min) & (cell_centers <= box_max), axis=1
+        )
+        coverage_count += inside
+        direction_field[inside] = direction
+
+    n_overlap = int(np.count_nonzero(coverage_count > 1))
+    if n_overlap:
+        raise ValueError(
+            f"{n_overlap} cells fall in more than one box; loop-direction "
+            f"boxes must not overlap"
+        )
+
+    covered = coverage_count > 0
+    if not np.any(covered):
+        raise ValueError(
+            "No cell falls within any loop box; the boxes and the mesh are in "
+            "different coordinate frames. For a block-rectangular case this "
+            "usually means the 'rescale' parameter is missing from mesh.json "
+            "(assumed 1.0) - supply the rescale used to build the mesh."
+        )
+
+    _report_coverage(covered)
+    return direction_field
+
+
+def build_loop_direction_field_from_path(
+    cell_centers: np.ndarray, path_points: np.ndarray, max_dist: float
+) -> np.ndarray:
+    """Per-cell loop-direction field from a centerline polyline.
+
+    Each cell within ``max_dist`` of the polyline gets the unit tangent of its
+    nearest segment; cells farther away keep ``NaN`` (excluded). The polyline
+    ordering sets the circulation sense.
+
+    Parameters
+    ----------
+    cell_centers: np.ndarray
+        Cell centres, shape ``(N, 3)``
+    path_points: np.ndarray
+        Ordered centerline vertices, shape ``(M, 3)``
+    max_dist: float
+        Cells beyond this distance from the path are left uncovered
+
+    Returns
+    ----------
+    direction_field: np.ndarray
+        Direction field, shape ``(N, 3)``, ``NaN`` where uncovered
+    """
+    cell_centers = np.asarray(cell_centers, dtype=float)
+    path_points = np.asarray(path_points, dtype=float)
+    if len(path_points) < 2:
+        raise ValueError("path_points must contain at least two vertices")
+
+    n_cells = len(cell_centers)
+    best_distance = np.full(n_cells, np.inf)
+    direction_field = np.full((n_cells, 3), np.nan)
+
+    for start, end in zip(path_points[:-1], path_points[1:]):
+        segment = end - start
+        length_sq = float(segment @ segment)
+        if length_sq == 0.0:
+            continue
+        tangent = segment / np.sqrt(length_sq)
+        # Projection parameter of each cell onto the segment, clamped to [0, 1]
+        param = np.clip(
+            ((cell_centers - start) @ segment) / length_sq, 0.0, 1.0
+        )
+        projection = start + param[:, None] * segment
+        distance = np.linalg.norm(cell_centers - projection, axis=1)
+        closer = distance < best_distance
+        best_distance[closer] = distance[closer]
+        direction_field[closer] = tangent
+
+    uncovered = best_distance > max_dist
+    direction_field[uncovered] = np.nan
+    if np.all(uncovered):
+        raise ValueError(
+            "No cell lies within max_dist of the path; the path and the mesh "
+            "are in different coordinate frames, or max_dist is too small"
+        )
+    _report_coverage(~uncovered)
+    return direction_field
+
+
+def propose_loop_boxes_block_rect(
+    mesh_geometry: dict, rescale: float | None = None
+) -> list[dict]:
+    """Candidate loop-direction boxes for a block-rectangular loop reactor.
+
+    Builds one box per mesh segment (leg) from
+    :func:`bird.meshing.block_rect_mesh.from_block_rect_to_seg`. Each box spans the
+    leg along its axis, trimmed half a block at each end so adjacent legs do not
+    overlap and the ambiguous junction cells stay uncovered. The proposed direction
+    is each leg's own axis orientation (``end - start``).
+
+    The mesh scale is never inferred: the box coordinates are scaled by ``rescale``,
+    which the caller must set to the factor used to build the mesh (e.g. the
+    ``transformPoints`` scale). A mismatch surfaces downstream as a zero-coverage
+    error in :func:`build_loop_direction_field`.
+
+    Parameters
+    ----------
+    mesh_geometry: dict
+        The ``"Geometry"`` dict from the case ``mesh.json``
+    rescale: float | None
+        Uniform scale factor applied to the box coordinates; ``None`` assumes
+        1.0 (base units)
+
+    Returns
+    ----------
+    boxes: list[dict]
+        Box list consumable by :func:`build_loop_direction_field`
+    """
+    factor = 1.0 if rescale is None else float(rescale)
+    segment_data = from_block_rect_to_seg(mesh_geometry, rescale=False)
+    segments = segment_data["segments"]
+    block_size = segment_data["blocksize"]
+
+    boxes = []
+    for segment in segments.values():
+        start = np.asarray(segment["start"], dtype=float)
+        end = np.asarray(segment["end"], dtype=float)
+        normal_dir = int(segment["normal_dir"])
+        max_rad = float(segment["max_rad"])
+
+        box_min = np.empty(3)
+        box_max = np.empty(3)
+        for axis in range(3):
+            if axis == normal_dir:
+                low = min(start[axis], end[axis]) + 0.5 * block_size[axis]
+                high = max(start[axis], end[axis]) - 0.5 * block_size[axis]
+            else:
+                low = start[axis] - max_rad
+                high = start[axis] + max_rad
+            box_min[axis] = low
+            box_max[axis] = high
+
+        boxes.append(
+            {
+                "min": (box_min * factor).tolist(),
+                "max": (box_max * factor).tolist(),
+                "direction": _normalize(end - start).tolist(),
+            }
+        )
+    return boxes
+
+
+def _read_liquid_fraction(
+    case_folder: str, time_folder: str, n_cells: int, field_dict: dict
+) -> tuple[np.ndarray | float, dict]:
+    """Liquid fraction from alpha.gas (1 - alpha.gas) or alpha.liquid."""
+    try:
+        alpha_gas, field_dict = read_field(
+            case_folder, time_folder, "alpha.gas", n_cells, field_dict
+        )
+        return 1.0 - np.asarray(alpha_gas), field_dict
+    except FileNotFoundError:
+        pass
+    try:
+        alpha_liquid, field_dict = read_field(
+            case_folder, time_folder, "alpha.liquid", n_cells, field_dict
+        )
+        return alpha_liquid, field_dict
+    except FileNotFoundError:
+        raise FileNotFoundError(
+            "Need alpha.gas or alpha.liquid to average over the liquid"
+        )
+
+
+def compute_loop_velocity(
+    case_folder: str,
+    time_folder: str,
+    loop_direction_field: np.ndarray,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Loop velocity: liquid velocity projected on the loop direction.
+
+    .. math::
+       \frac{\int_{V_{\rm loop}} \alpha_{\rm liq}\, (\mathbf{U}_{\rm liq} \cdot
+       \hat{\mathbf{e}}_{\rm loop})\, dV}{\int_{V_{\rm loop}} \alpha_{\rm liq}\, dV}
+
+    Averaged over the liquid on the covered cells. Positive follows the prescribed
+    circulation, negative is reversed.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    loop_direction_field: np.ndarray
+        ``(N, 3)`` field from a builder, ``NaN`` on uncovered cells
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    loop_velocity: float
+        Volume averaged loop velocity, in :math:`m.s^{-1}`
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+
+    loop_direction_field = np.asarray(loop_direction_field, dtype=float)
+    n_cells = len(loop_direction_field)
+    covered = ~np.isnan(loop_direction_field).any(axis=1)
+    if not np.any(covered):
+        raise ValueError("The loop-direction field covers no cell")
+
+    u_liquid, field_dict = read_field(
+        case_folder, time_folder, "U.liquid", n_cells, field_dict
+    )
+    # A uniform vector field is read as shape (3,); broadcast to one per cell
+    if np.ndim(u_liquid) == 1:
+        u_liquid = np.broadcast_to(u_liquid, (n_cells, 3))
+
+    cell_volume, field_dict = read_cell_volumes(
+        case_folder, volume_time, n_cells, field_dict
+    )
+    alpha_liquid, field_dict = _read_liquid_fraction(
+        case_folder, time_folder, n_cells, field_dict
+    )
+
+    # Liquid velocity projected on the loop direction, averaged over the liquid
+    weights = np.asarray(cell_volume) * np.asarray(alpha_liquid)
+    if weights.ndim == 0:
+        weights = np.full(n_cells, float(weights))
+    projected = np.sum(
+        u_liquid[covered] * loop_direction_field[covered], axis=1
+    )
+    loop_velocity = _weighted_average(projected, weights[covered])
+
+    return float(loop_velocity), field_dict
diff --git a/bird/postprocess/post_quantities/phase.py b/bird/postprocess/post_quantities/phase.py
index 23e30b8c..bfbdd0c5 100644
--- a/bird/postprocess/post_quantities/phase.py
+++ b/bird/postprocess/post_quantities/phase.py
@@ -1,12 +1,45 @@
+import os
+
+import numpy as np
+
+from bird import logger
 from bird.utilities.ofio import (
     read_bubble_diameter,
     read_cell_volumes,
     read_field,
+    read_global_vars,
 )
 
 from ._cell_filter import _field_filter, _get_ind_liq, _weighted_average
 
 
+def _read_liquid_density_field(
+    case_folder: str,
+    time_folder: str,
+    n_cells: int | None,
+    field_dict: dict,
+) -> tuple[np.ndarray | float, dict]:
+    """Liquid density field: thermo:rho.liquid, then rho.liquid; if neither is
+    written, globalVars rho0MixLiq (then 1000)."""
+    for rho_name in ("thermo:rho.liquid", "rho.liquid"):
+        try:
+            rho_liquid, field_dict = read_field(
+                case_folder, time_folder, rho_name, n_cells, field_dict
+            )
+            return rho_liquid, field_dict
+        except FileNotFoundError:
+            continue
+    try:
+        rho0 = float(read_global_vars(case_folder).get("rho0MixLiq", 1000.0))
+    except FileNotFoundError:
+        rho0 = 1000.0
+    logger.warning(
+        f"No liquid density field in "
+        f"{os.path.join(case_folder, time_folder)}, assuming {rho0} kg/m3"
+    )
+    return rho0, field_dict
+
+
 def compute_gas_holdup(
     case_folder: str,
     time_folder: str,
@@ -157,3 +190,124 @@ def compute_ave_bubble_diam(
     diam = _weighted_average(d_gas, alpha_liq * cell_volume)
 
     return diam, field_dict
+
+
+def interfacial_area(gas_holdup: float, bubble_diam: float) -> float:
+    r"""Gas-liquid interfacial area per unit volume :math:`a = 6\,\epsilon / d`.
+
+    Parameters
+    ----------
+    gas_holdup: float
+        Gas holdup :math:`\epsilon` (dimensionless)
+    bubble_diam: float
+        Bubble diameter :math:`d`, in :math:`m`
+
+    Returns
+    ----------
+    interfacial_area: float
+        Interfacial area :math:`a`, in :math:`m^{-1}`
+    """
+    return 6.0 * gas_holdup / bubble_diam
+
+
+def compute_ave_liquid_density(
+    case_folder: str,
+    time_folder: str,
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Volume-averaged liquid density over the liquid.
+
+    Reads ``thermo:rho.liquid`` (then ``rho.liquid``); returns 1000 kg/m3 if
+    neither field is written.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    density: float
+        Volume averaged liquid density, in :math:`kg.m^{-3}`
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+
+    ind_liq, field_dict = _get_ind_liq(
+        case_folder, time_folder, n_cells=n_cells, field_dict=field_dict
+    )
+    rho_liquid, field_dict = _read_liquid_density_field(
+        case_folder, time_folder, n_cells, field_dict
+    )
+    cell_volume, field_dict = read_cell_volumes(
+        case_folder, volume_time, n_cells, field_dict
+    )
+    rho_liquid = _field_filter(rho_liquid, ind=ind_liq, field_type="scalar")
+    cell_volume = _field_filter(cell_volume, ind=ind_liq, field_type="scalar")
+    return _weighted_average(rho_liquid, cell_volume), field_dict
+
+
+def compute_ave_liquid_velocity(
+    case_folder: str,
+    time_folder: str,
+    n_cells: int | None = None,
+    volume_time: str | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Volume-averaged liquid velocity magnitude :math:`|U_{\rm liq}|` over the liquid.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    volume_time : str | None
+        Time folder to read to get the cell volumes.
+        If None, finds volume time automatically
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    velocity_magnitude: float
+        Volume averaged liquid velocity magnitude, in :math:`m.s^{-1}`
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+
+    ind_liq, field_dict = _get_ind_liq(
+        case_folder, time_folder, n_cells=n_cells, field_dict=field_dict
+    )
+    u_liquid, field_dict = read_field(
+        case_folder, time_folder, "U.liquid", n_cells, field_dict
+    )
+    cell_volume, field_dict = read_cell_volumes(
+        case_folder, volume_time, n_cells, field_dict
+    )
+    if np.ndim(u_liquid) == 1:  # uniform field, shape (3,)
+        u_magnitude = float(np.linalg.norm(u_liquid))
+    else:
+        u_magnitude = np.linalg.norm(u_liquid, axis=1)
+    u_magnitude = _field_filter(u_magnitude, ind=ind_liq, field_type="scalar")
+    cell_volume = _field_filter(cell_volume, ind=ind_liq, field_type="scalar")
+    return _weighted_average(u_magnitude, cell_volume), field_dict
diff --git a/bird/postprocess/post_quantities/species.py b/bird/postprocess/post_quantities/species.py
index a3f8da37..476cfb0c 100644
--- a/bird/postprocess/post_quantities/species.py
+++ b/bird/postprocess/post_quantities/species.py
@@ -1,5 +1,3 @@
-import os
-
 from bird import logger
 from bird.utilities.ofio import (
     read_cell_volumes,
@@ -8,6 +6,7 @@
 )
 
 from ._cell_filter import _field_filter, _get_ind_liq, _weighted_average
+from .phase import _read_liquid_density_field
 
 
 def compute_ave_y_liq(
@@ -168,17 +167,9 @@ def compute_ave_conc_liq(
     cell_volume, field_dict = read_cell_volumes(
         field_dict=field_dict, **kwargs_vol
     )
-    try:
-        rho_liq, field_dict = read_field(
-            field_name="thermo:rho.liquid", field_dict=field_dict, **kwargs
-        )
-    except FileNotFoundError:
-        abs_time_path = os.path.join(case_folder, time_folder)
-        logger.warning(
-            f"thermo:rho.liquid not found in {abs_time_path}, assuming it is 1000kg/m3"
-        )
-        rho_liq = 1000.0
-        field_dict["rho_liq"] = rho_liq
+    rho_liq, field_dict = _read_liquid_density_field(
+        case_folder, time_folder, n_cells, field_dict
+    )
 
     # Only compute over the liquid
     alpha_liq = _field_filter(alpha_liq, ind=ind_liq, field_type="scalar")
diff --git a/bird/postprocess/post_quantities/transport.py b/bird/postprocess/post_quantities/transport.py
new file mode 100644
index 00000000..6371b4a9
--- /dev/null
+++ b/bird/postprocess/post_quantities/transport.py
@@ -0,0 +1,78 @@
+import numpy as np
+
+from bird.utilities.ofio import read_cell_volumes, read_field
+
+from ._cell_filter import _field_filter, _get_ind_liq, _weighted_average
+from .phase import _read_liquid_density_field
+
+# Turbulent Prandtl (= turbulent Schmidt) for the nut/Prt fallback
+TURBULENT_PRANDTL = 0.85
+
+
+def compute_turbulent_diffusivity(
+    case_folder: str,
+    time_folder: str,
+    n_cells: int | None = None,
+    field_dict: dict | None = None,
+) -> tuple[float, dict]:
+    r"""Liquid-averaged turbulent mass diffusivity.
+
+    .. math::
+       D_{\rm turb} = \frac{\alpha_t^{\rm liq}}{\rho^{\rm liq}}
+
+    averaged over the liquid [m^2/s]. ``alphat.liquid`` already carries the
+    solver's turbulent Prandtl number; if it was not written, the field falls
+    back to :math:`\nu_t^{\rm liq} / Pr_t` with :math:`Pr_t = 0.85`. The density
+    is read from ``thermo:rho.liquid`` (then ``rho.liquid``), falling back to
+    ``rho0MixLiq`` from ``globalVars`` and then 1000.
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+    time_folder: str
+        Name of the time folder to analyze
+    n_cells : int | None
+        Number of cells in the domain.
+        If None, it will deduced from the field reading
+    field_dict : dict
+        Dictionary of fields used to avoid rereading the same fields to calculate different quantities
+
+    Returns
+    ----------
+    turbulent_diffusivity: float
+        Volume averaged turbulent mass diffusivity, in :math:`m^2.s^{-1}`
+    field_dict : dict
+        Dictionary of fields read
+    """
+    if field_dict is None:
+        field_dict = {}
+
+    ind_liq, field_dict = _get_ind_liq(
+        case_folder, time_folder, n_cells=n_cells, field_dict=field_dict
+    )
+    cell_volume, field_dict = read_cell_volumes(
+        case_folder, time_folder, n_cells, field_dict
+    )
+
+    rho_liquid, field_dict = _read_liquid_density_field(
+        case_folder, time_folder, n_cells, field_dict
+    )
+
+    # Turbulent diffusivity field: alphat.liquid / rho, else nut.liquid / Prt
+    try:
+        alphat_liquid, field_dict = read_field(
+            case_folder, time_folder, "alphat.liquid", n_cells, field_dict
+        )
+        diffusivity = np.asarray(alphat_liquid) / np.asarray(rho_liquid)
+    except FileNotFoundError:
+        nut_liquid, field_dict = read_field(
+            case_folder, time_folder, "nut.liquid", n_cells, field_dict
+        )
+        diffusivity = np.asarray(nut_liquid) / TURBULENT_PRANDTL
+    if diffusivity.ndim == 0:
+        diffusivity = float(diffusivity)
+
+    diffusivity = _field_filter(diffusivity, ind=ind_liq, field_type="scalar")
+    cell_volume = _field_filter(cell_volume, ind=ind_liq, field_type="scalar")
+    return _weighted_average(diffusivity, cell_volume), field_dict
diff --git a/bird/postprocess/stats.py b/bird/postprocess/stats.py
index 8f5a941e..963556e1 100644
--- a/bird/postprocess/stats.py
+++ b/bird/postprocess/stats.py
@@ -184,3 +184,56 @@ def calc_mean(
     unc_val = np.sqrt(sigsq * T0 / N)
 
     return mean_val, unc_val * 1.96
+
+
+def steady_stat(
+    time_series: np.ndarray | list,
+    time_values: np.ndarray | list,
+    window: float | None = None,
+) -> tuple[float, float]:
+    """(mean, 1-sigma uncertainty) over the tail window of a time series.
+
+    The statistic is computed over the last ``window`` (in time units) of the
+    series via the T0 estimator (:func:`calc_mean`), with its 95% (1.96 sigma)
+    uncertainty converted to 1 sigma. ``window`` defaults to 10% of the total
+    simulation time. Returns (nan, nan) for an empty or all-nan series and
+    (value, 0.0) when a single sample falls in the window.
+
+    Parameters
+    ----------
+    time_series: np.ndarray | list
+        Time series of the signal
+    time_values: np.ndarray | list
+        Sampling times of the series
+    window: float | None
+        Length of the end window in time units.
+        If None, 10% of the total time span is used
+
+    Returns
+    ----------
+    mean_val: float
+        Mean value over the tail window
+    unc_val: float
+        1-sigma uncertainty about the mean
+    """
+    time_series = np.asarray(time_series, dtype=float)
+    time_values = np.asarray(time_values, dtype=float)
+    if time_series.size == 0 or np.all(np.isnan(time_series)):
+        return np.nan, np.nan
+
+    if window is None:
+        window = 0.1 * (time_values.max() - time_values.min())
+        logger.warning(f"Steady state assumed over last {window}s")
+
+    in_window = time_values >= time_values.max() - window
+    windowed_series = time_series[in_window]
+    windowed_values = time_values[in_window]
+    if np.all(np.isnan(windowed_series)):
+        return np.nan, np.nan
+    if windowed_series.size < 2 or np.all(
+        windowed_series == windowed_series[0]
+    ):
+        return float(windowed_series[0]), 0.0
+
+    mean_value, uncertainty_95 = calc_mean(windowed_series, windowed_values)
+    return float(mean_value), float(uncertainty_95 / 1.96)
diff --git a/bird/preprocess/dynamic_mixer/io_fvModels.py b/bird/preprocess/dynamic_mixer/io_fvModels.py
index f8b02d38..b78fb49c 100644
--- a/bird/preprocess/dynamic_mixer/io_fvModels.py
+++ b/bird/preprocess/dynamic_mixer/io_fvModels.py
@@ -374,11 +374,16 @@ def write_mixer_ball(
 ):
     """Append one ``ball`` mixer block to ``fvModels``.
 
-    :param mixer: a ready :class:`~bird.preprocess.dynamic_mixer.mixer.ActuatorMixer`.
-    :param power_mode: ``"from_P"`` (drive by ``mixer.power``) or
-        ``"from_Np_Vtip"`` (drive by ``mixer.Np`` and ``mixer.Vtip``).
-    :param momentum_mode: ``"axial"`` (thrust only) or ``"axial_and_swirl"``
-        (thrust + tangential source using ``mixer.sigma``).
+    Parameters
+    ----------
+    mixer: ActuatorMixer
+        A ready :class:`~bird.preprocess.dynamic_mixer.mixer.ActuatorMixer`.
+    power_mode: str
+        ``"from_P"`` (drive by ``mixer.power``) or ``"from_Np_Vtip"`` (drive by
+        ``mixer.Np`` and ``mixer.Vtip``).
+    momentum_mode: str
+        ``"axial"`` (thrust only) or ``"axial_and_swirl"`` (thrust + tangential
+        source using ``mixer.sigma``).
     """
     if power_mode not in ("from_P", "from_Np_Vtip"):
         raise ValueError(f"unknown power_mode {power_mode!r}")
@@ -542,8 +547,10 @@ def write_static_mixer_ball(mixer, output_folder):
     energy-neutral axial reaction; a lumped axial drag adds the viscous loss.
     The source is inactive when the inflow opposes the mixer orientation.
 
-    :param mixer: a ready
-        :class:`~bird.preprocess.dynamic_mixer.mixer.StaticMixer`.
+    Parameters
+    ----------
+    mixer: StaticMixer
+        A ready :class:`~bird.preprocess.dynamic_mixer.mixer.StaticMixer`.
     """
     nd = int(mixer.normal_dir)
     dn = ["dx", "dy", "dz"][nd]
diff --git a/bird/preprocess/dynamic_mixer/mixer.py b/bird/preprocess/dynamic_mixer/mixer.py
index 92c99dd5..d8a190f0 100644
--- a/bird/preprocess/dynamic_mixer/mixer.py
+++ b/bird/preprocess/dynamic_mixer/mixer.py
@@ -171,10 +171,13 @@ def update_from_expl_dict(self, mixer_dict: dict) -> None:
     def update_from_loop_dict(self, mixer_dict: dict, geom_dict: dict) -> None:
         """Populate from a loop mixer dict.
 
-        :param mixer_dict: mixer entry with ``branch_id``, ``frac_space`` and,
-            optionally, ``radius`` as a fraction of the branch cross-section.
-        :param geom_dict: output of ``from_block_rect_to_seg`` (``segments`` and
-            ``blocksize``).
+        Parameters
+        ----------
+        mixer_dict: dict
+            Mixer entry with ``branch_id``, ``frac_space`` and, optionally,
+            ``radius`` as a fraction of the branch cross-section.
+        geom_dict: dict
+            Output of ``from_block_rect_to_seg`` (``segments`` and ``blocksize``).
         """
         segment = geom_dict["segments"][mixer_dict["branch_id"]]
         pos = segment["start"] + mixer_dict["frac_space"] * segment["conn"]
@@ -274,11 +277,14 @@ def update_from_expl_dict(self, mixer_dict: dict) -> None:
     def update_from_loop_dict(self, mixer_dict: dict, geom_dict: dict) -> None:
         """Populate from a loop mixer dict.
 
-        :param mixer_dict: mixer entry with ``branch_id``, ``frac_space`` and,
-            optionally, ``radius`` as a fraction of the branch cross-section
-            (``0.5`` spans the whole tube).
-        :param geom_dict: output of ``from_block_rect_to_seg`` (``segments`` and
-            ``blocksize``).
+        Parameters
+        ----------
+        mixer_dict: dict
+            Mixer entry with ``branch_id``, ``frac_space`` and, optionally,
+            ``radius`` as a fraction of the branch cross-section (``0.5`` spans
+            the whole tube).
+        geom_dict: dict
+            Output of ``from_block_rect_to_seg`` (``segments`` and ``blocksize``).
         """
         segment = geom_dict["segments"][mixer_dict["branch_id"]]
         pos = segment["start"] + mixer_dict["frac_space"] * segment["conn"]
diff --git a/bird/preprocess/json_gen/design_io.py b/bird/preprocess/json_gen/design_io.py
index 7846bbff..7607f8e1 100644
--- a/bird/preprocess/json_gen/design_io.py
+++ b/bird/preprocess/json_gen/design_io.py
@@ -13,8 +13,11 @@ def generate_stl_patch(filename, bc_dict, geom_dict):
 def generate_dynamic_mixer(filename, mixers_list, geom_dict, model=None):
     """Write a mixers.json.
 
-    :param model: optional dict of top-level model selectors written verbatim
-        (e.g. ``{"volumetric_source": "ball", "power": "from_Np_Vtip",
+    Parameters
+    ----------
+    model:
+        Optional dict of top-level model selectors written verbatim (e.g.
+        ``{"volumetric_source": "ball", "power": "from_Np_Vtip",
         "momentum_source": "axial_and_swirl"}``). ``None`` keeps the legacy
         pancake output.
     """
diff --git a/bird/preprocess/json_gen/generate_designs.py b/bird/preprocess/json_gen/generate_designs.py
index 254b722f..f05b1040 100644
--- a/bird/preprocess/json_gen/generate_designs.py
+++ b/bird/preprocess/json_gen/generate_designs.py
@@ -87,11 +87,18 @@ def sample_placement_designs(
     :func:`check_config` keeps only designs with at least one inlet and
     :func:`compare_config` rejects duplicates. Keys are contiguous ``0..n-1``.
 
-    :param branches_com: branch ids on which choices are placed.
-    :param branchcom_spots: ``branch_id -> array`` of candidate spot fractions.
-    :param n_designs: number of distinct valid designs to return.
-    :param choices: per-spot categorical choices (e.g. mixer/sparger/none).
-    :param max_attempts: give up after this many draws.
+    Parameters
+    ----------
+    branches_com:
+        Branch ids on which choices are placed.
+    branchcom_spots:
+        ``branch_id -> array`` of candidate spot fractions.
+    n_designs:
+        Number of distinct valid designs to return.
+    choices:
+        Per-spot categorical choices (e.g. mixer/sparger/none).
+    max_attempts:
+        Give up after this many draws.
     """
     config_dict = {}
     attempts = 0
@@ -706,9 +713,14 @@ def overwrite_qoi_params(case_folder, rhog, cstar_co2, cstar_h2):
     own values (the mixer power is NOT touched here -- get_qoi.py reads it from
     mixers.json).
 
-    :param rhog: gas density [kg/m3] used in the injection-power estimate.
-    :param cstar_co2: (low, high) uniform-prior bounds for the CO2 c*.
-    :param cstar_h2: (low, high) uniform-prior bounds for the H2 c*.
+    Parameters
+    ----------
+    rhog:
+        Gas density in :math:`kg.m^{-3}` used in the injection-power estimate.
+    cstar_co2:
+        (low, high) uniform-prior bounds for the CO2 c*.
+    cstar_h2:
+        (low, high) uniform-prior bounds for the H2 c*.
     """
     co2_lo, co2_hi = cstar_co2
     h2_lo, h2_hi = cstar_h2
@@ -751,8 +763,11 @@ def overwrite_ncores(case_folder, n):
 def overwrite_controldict(case_folder, params):
     """Rewrite time-stepping entries in system/controlDict.
 
-    :param params: dict with any of ``deltaT``, ``endTime``, ``maxCo``,
-        ``maxDeltaT``; each present key overwrites its scalar entry.
+    Parameters
+    ----------
+    params:
+        Dict with any of ``deltaT``, ``endTime``, ``maxCo``, ``maxDeltaT``;
+        each present key overwrites its scalar entry.
     """
     filename = os.path.join(case_folder, "system", "controlDict")
     with open(filename, "r+") as f:
diff --git a/bird/utilities/ofio/__init__.py b/bird/utilities/ofio/__init__.py
index ec90e6d5..66618409 100644
--- a/bird/utilities/ofio/__init__.py
+++ b/bird/utilities/ofio/__init__.py
@@ -4,6 +4,7 @@
     get_case_times,
 )
 from .foam_dict_io import (
+    read_gravity,
     read_openfoam_dict,
     write_openfoam_dict,
 )
@@ -24,6 +25,7 @@
 )
 from .global_vars import (
     read_global_vars,
+    read_surface_tension,
 )
 from .thermo import (
     get_species_name,
@@ -39,10 +41,12 @@
     "read_cell_volumes",
     "read_field",
     "read_global_vars",
+    "read_gravity",
     "read_mu_liquid",
     "read_openfoam_dict",
     "read_size_groups",
     "read_surface_field_value",
+    "read_surface_tension",
     "species_name_to_mw",
     "write_openfoam_dict",
 ]
diff --git a/bird/utilities/ofio/foam_dict_io.py b/bird/utilities/ofio/foam_dict_io.py
index fe1ebc8a..a2c94b96 100644
--- a/bird/utilities/ofio/foam_dict_io.py
+++ b/bird/utilities/ofio/foam_dict_io.py
@@ -1,3 +1,4 @@
+import os
 import re
 
 
@@ -193,6 +194,16 @@ def read_openfoam_dict(filename: str) -> dict:
     return foam_dict
 
 
+def read_gravity(case_folder: str) -> float:
+    """Gravity magnitude [m/s2] from constant/g; 9.81 if the file is absent."""
+    try:
+        g_dict = read_openfoam_dict(os.path.join(case_folder, "constant", "g"))
+    except FileNotFoundError:
+        return 9.81
+    gravity_vector = [float(component) for component in g_dict["value"]]
+    return sum(component**2 for component in gravity_vector) ** 0.5
+
+
 def write_openfoam_dict(data: dict, filename: str, indent: int = 0) -> None:
     """
     Save a Python dictionary back to an OpenFOAM-style file.
diff --git a/bird/utilities/ofio/global_vars.py b/bird/utilities/ofio/global_vars.py
index ec2f9bd0..eb3fdfc4 100644
--- a/bird/utilities/ofio/global_vars.py
+++ b/bird/utilities/ofio/global_vars.py
@@ -6,6 +6,8 @@
 
 from bird import logger
 
+from .foam_dict_io import read_openfoam_dict
+
 
 def _cross_reference_math(expr):
     """
@@ -207,3 +209,24 @@ def read_global_vars(
         globalVars_dict = _cross_reference_global_vars(globalVars_dict)
 
     return globalVars_dict
+
+
+def read_surface_tension(case_folder: str) -> float:
+    """Surface tension [N/m] from constant/phaseProperties.
+
+    Resolves a ``$var`` reference (e.g. ``sigma $sigmaLiq;``) against globalVars.
+    """
+    phase_properties = read_openfoam_dict(
+        os.path.join(case_folder, "constant", "phaseProperties")
+    )
+    sigma = None
+    for entry in phase_properties["surfaceTension"].values():
+        if isinstance(entry, dict) and "sigma" in entry:
+            sigma = entry["sigma"]
+            break
+    if sigma is None:
+        raise KeyError("No sigma found in surfaceTension of phaseProperties")
+
+    if isinstance(sigma, str) and sigma.startswith("$"):
+        return float(read_global_vars(case_folder, cross_ref=True)[sigma[1:]])
+    return float(sigma)
diff --git a/bird/version.py b/bird/version.py
index cfeacc5a..57285602 100644
--- a/bird/version.py
+++ b/bird/version.py
@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.57"
+__version__ = "0.0.59"
diff --git a/papers/scaleup/SA_optimization/README.md b/papers/scaleup/SA_optimization/README.md
new file mode 100644
index 00000000..ff88756f
--- /dev/null
+++ b/papers/scaleup/SA_optimization/README.md
@@ -0,0 +1,19 @@
+
+# Optim
+
+`python get_optimal_all_qois.py --plot-only` regenerates the optimization plots
+
+`python get_optimal_all_qois.py` recomputes the optimization
+
+# Constrained optim
+
+`python get_optimal_constrained.py` redoes the constrained optimization (constrains the number of spargers)
+
+`python plot_marginal_gain.py` plots the results of the constrained optimization
+
+# Latex tables
+
+`python make_hyperparam_tables.py` makes the latex tables with the optimal hyperpar
+
+`python make_val_rmse_table.py` makes the surrogate perf tables
+
diff --git a/papers/scaleup/SA_optimization/configs.pkl b/papers/scaleup/SA_optimization/configs.pkl
new file mode 100644
index 00000000..b4bd9b37
Binary files /dev/null and b/papers/scaleup/SA_optimization/configs.pkl differ
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/X_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/X_data.csv
new file mode 100644
index 00000000..7e52590c
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/X_data.csv
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/Y_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/Y_data.csv
new file mode 100644
index 00000000..ad313b36
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/Y_data.csv
@@ -0,0 +1,290 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/best_bootstrap_solution_nn_qoi.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/best_bootstrap_solution_nn_qoi.csv
new file mode 100644
index 00000000..43e0a38f
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/best_bootstrap_solution_nn_qoi.csv
@@ -0,0 +1,2 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/convergence_data_nn_qoi.npz b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/convergence_data_nn_qoi.npz
new file mode 100644
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/hyperparams_qoi.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/hyperparams_qoi.json
new file mode 100644
index 00000000..631a1b8d
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/hyperparams_qoi.json
@@ -0,0 +1,50 @@
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+  "qoi": "qoi",
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+}
\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv
new file mode 100644
index 00000000..05846359
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/hyperparams_qoi_kla.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/hyperparams_qoi_kla.json
new file mode 100644
index 00000000..01d9c99f
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/hyperparams_qoi_kla.json
@@ -0,0 +1,50 @@
+{
+  "qoi": "qoi_kla",
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\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv
new file mode 100644
index 00000000..29998b1c
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/hyperparams_qoi_sum.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/hyperparams_qoi_sum.json
new file mode 100644
index 00000000..a4e444cd
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/hyperparams_qoi_sum.json
@@ -0,0 +1,50 @@
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\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum_kla/best_bootstrap_solution_nn_qoi_sum_kla.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum_kla/best_bootstrap_solution_nn_qoi_sum_kla.csv
new file mode 100644
index 00000000..99d0e9ba
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+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum_kla/best_bootstrap_solution_nn_qoi_sum_kla.csv
@@ -0,0 +1,2 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev3/X_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev3/X_data.csv
new file mode 100644
index 00000000..53023e58
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev3/X_data.csv
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev3/Y_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev3/Y_data.csv
new file mode 100644
index 00000000..0cdc4075
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev3/Y_data.csv
@@ -0,0 +1,149 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev4/X_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev4/X_data.csv
new file mode 100644
index 00000000..34157e56
--- /dev/null
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev4/Y_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev4/Y_data.csv
new file mode 100644
index 00000000..1c41a34c
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev4/Y_data.csv
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev5/X_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev5/X_data.csv
new file mode 100644
index 00000000..ef7b8dc3
--- /dev/null
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev5/Y_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev5/Y_data.csv
new file mode 100644
index 00000000..4cbf0284
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev5/Y_data.csv
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/X_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/X_data.csv
new file mode 100644
index 00000000..65a57991
--- /dev/null
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/Y_data.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/Y_data.csv
new file mode 100644
index 00000000..d5b7754a
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/Y_data.csv
@@ -0,0 +1,302 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/best_bootstrap_solution_nn_qoi.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/best_bootstrap_solution_nn_qoi.csv
new file mode 100644
index 00000000..c0c9df82
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/best_bootstrap_solution_nn_qoi.csv
@@ -0,0 +1,2 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/cfd_all_spargers.txt b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/cfd_all_spargers.txt
new file mode 100644
index 00000000..6126fed6
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/convergence_data_nn_qoi.npz b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/convergence_data_nn_qoi.npz
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/hyperparams_qoi.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/hyperparams_qoi.json
new file mode 100644
index 00000000..3d1b9fb9
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/hyperparams_qoi.json
@@ -0,0 +1,50 @@
+{
+  "qoi": "qoi",
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+  "best_params": {
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+}
\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv
new file mode 100644
index 00000000..459e1ba1
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv
@@ -0,0 +1,2 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/cfd_all_spargers.txt b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/cfd_all_spargers.txt
new file mode 100644
index 00000000..9dec85f5
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/hyperparams_qoi_kla.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/hyperparams_qoi_kla.json
new file mode 100644
index 00000000..908a5901
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/hyperparams_qoi_kla.json
@@ -0,0 +1,50 @@
+{
+  "qoi": "qoi_kla",
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\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv
new file mode 100644
index 00000000..53acf3eb
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv
@@ -0,0 +1,2 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/cfd_all_spargers.txt b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/cfd_all_spargers.txt
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/hyperparams_qoi_sum.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/hyperparams_qoi_sum.json
new file mode 100644
index 00000000..1d883938
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/hyperparams_qoi_sum.json
@@ -0,0 +1,50 @@
+{
+  "qoi": "qoi_sum",
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\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/best_bootstrap_solution_rbf_qoi_sum_kla.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/best_bootstrap_solution_rbf_qoi_sum_kla.csv
new file mode 100644
index 00000000..a5762411
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/best_bootstrap_solution_rbf_qoi_sum_kla.csv
@@ -0,0 +1,2 @@
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/cfd_all_spargers.txt b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/cfd_all_spargers.txt
new file mode 100644
index 00000000..c4819b87
--- /dev/null
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diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/hyperparams_qoi_sum_kla.json b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/hyperparams_qoi_sum_kla.json
new file mode 100644
index 00000000..d5778cbb
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/hyperparams_qoi_sum_kla.json
@@ -0,0 +1,49 @@
+{
+  "qoi": "qoi_sum_kla",
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+}
\ No newline at end of file
diff --git a/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/split.csv b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/split.csv
new file mode 100644
index 00000000..60b701c5
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/split.csv
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+0,1,2,1,1,0,2,2,1,1,1
+0,2,0,0,2,2,1,2,0,0,0
+1,2,0,2,1,0,0,0,2,0,0
+0,2,0,0,2,1,0,2,1,1,0
+0,0,2,1,1,1,1,1,1,1,2
+0,0,1,2,0,2,0,0,0,1,1
+0,2,2,0,0,1,0,1,1,1,2
+1,0,1,0,2,1,1,2,2,1,0
+1,1,2,0,1,0,0,2,1,0,0
+1,0,1,0,2,2,1,2,1,0,0
+2,2,1,2,2,1,0,0,1,2,0
+2,2,0,2,2,2,1,0,0,2,2
+2,1,2,2,2,0,2,1,1,0,0
+2,1,0,1,1,2,0,1,2,0,2
+2,2,1,0,1,0,2,1,2,0,0
+1,0,1,2,0,1,0,0,1,1,2
+2,2,0,2,2,2,1,2,1,2,2
+2,1,0,1,2,0,2,1,2,0,1
+1,0,1,2,2,0,1,0,0,0,0
+2,0,2,2,1,2,1,0,1,1,2
+2,2,2,0,2,2,2,0,1,2,0
+2,0,1,0,2,0,2,0,0,2,1
+2,0,1,2,1,2,1,1,1,1,2
+0,0,0,0,0,1,2,1,0,2,0
diff --git a/papers/scaleup/SA_optimization/data/study_pbe/study_0_4vvm_lev6/Y_data.csv b/papers/scaleup/SA_optimization/data/study_pbe/study_0_4vvm_lev6/Y_data.csv
new file mode 100644
index 00000000..52e303c6
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/study_pbe/study_0_4vvm_lev6/Y_data.csv
@@ -0,0 +1,27 @@
+sim_id,qoi,qoi_err,qoi_kla,qoi_kla_err,qoi_sum,qoi_sum_err,qoi_sum_kla,qoi_sum_kla_err
+0,15.60790946135167,1.7432990949938365,0.23880492063823605,0.02667291241402799,34.43614877224197,3.0221121137636353,4.259551196452832,0.37381768080793437
+2,10.280736665444925,1.1614613732476446,0.16183426219697342,0.018283149401306202,29.82979689595385,2.5145712696327718,3.7426000142633358,0.3154910676200518
+3,13.890486458464714,1.3754173656826874,0.21252791890893571,0.021044229893159638,32.25662808328225,2.632227666614026,3.98995717129763,0.3255912436904034
+5,10.155493474984649,1.0754837162138284,0.16441066663059156,0.017411364122148557,31.13729132418198,2.614826178802271,3.9618251937834037,0.33270344952895103
+6,5.406433697753096,0.5604007760264605,0.08752503727590803,0.009072357408461051,21.922485498780485,1.3944086680817644,2.789333886920631,0.17741926891969867
+8,6.926839310317702,0.7689541110293998,0.11058330688269447,0.012275943562313343,24.093050096991668,2.059792290348181,3.044170784705605,0.2602559446644207
+11,10.403033000538139,0.4656125471511252,0.15916898035125096,0.007123987241505401,30.35140895165187,0.5551754571072282,3.754292323215717,0.06867196708975204
+12,8.926217805968637,0.909873081510398,0.14450654154685788,0.014729935468046976,25.279218506147217,1.8420593380765384,3.216426692585517,0.2343762653451896
+14,6.926422173484384,0.8063622175612021,0.10903218126624155,0.012693339976871932,24.327533799872462,1.8173615919931856,3.0522559956572644,0.22801541911607637
+15,14.124077292986918,1.4064458015151453,0.21920684450548122,0.021828154839622693,33.369209133543535,2.6690886135431913,4.157123495092597,0.33251405334299117
+16,9.638167713814703,0.9287088994918005,0.15386804908523652,0.014826327033931884,27.84223630660519,1.9966754566894844,3.5178806340163526,0.2522809534461616
+17,10.015735746484058,0.9973088048133367,0.15766256922743532,0.015699123105879734,28.16472850807644,2.07032339864447,3.5336899400499893,0.2597532926455223
+18,11.25672914215921,1.1855801089917835,0.1747056582704815,0.018400331993247962,31.110778826626266,2.7341202980630497,3.8757723550153353,0.34061596225452656
+19,8.95724851218112,1.1355191036740961,0.13902038915508455,0.017623749912836363,29.542513249186133,2.493773500736249,3.680436907227945,0.3106768863217681
+20,11.614260664867116,1.1959386605983566,0.18025458631505828,0.018561097838663693,30.384676032181773,2.502742727238163,3.7853146665951796,0.3117910074833462
+24,9.827162935711282,1.2955559360202005,0.15251846037069286,0.020107145671500053,30.9137109469144,2.632990432271123,3.8512194804005135,0.32801704272527166
+28,10.452922836781427,1.240517257266111,0.16454473158312397,0.0195276079531394,30.524962835744162,2.7589764777369403,3.8298191148575977,0.3461554043075325
+29,14.446558450669665,1.6160678807449629,0.22741018503884852,0.025439297328182404,32.640270069811116,2.8462088166540975,4.0952130430868925,0.35709972510586585
+31,6.9598773796084785,0.8034756421560996,0.1049693633620242,0.012118076516854358,26.109891488646294,1.962722353377068,3.2065318232376434,0.2410401318220777
+32,13.57625322889985,1.4429836418082933,0.21070468187211167,0.02239523704129638,32.24999517908005,2.674264448681398,4.017693310575925,0.3331589454980116
+33,6.378568457922549,0.6972596778201505,0.10326264582720857,0.011287937040309807,22.501107613021304,1.672835748548624,2.8629509698514513,0.21284493239514765
+34,9.153801435682793,0.5637244250084206,0.14005556843785827,0.008625131901932061,29.32121619567555,0.8289825922448344,3.626865302404722,0.10254036463036421
+35,4.998160552643469,0.5785616116864034,0.07757362365721504,0.00897952761916296,20.481387283111072,1.3805487881306613,2.551592446863598,0.17199019830192944
+36,11.117276204636264,1.2184661351127752,0.17748197831973123,0.01945222698391056,27.789132922857107,2.340278963421366,3.511178663639579,0.2956960760935039
+37,11.020457794430056,1.3243366233510556,0.16621043930452992,0.0199736323172989,31.746201449667115,2.6903368856346006,3.898711495905444,0.3303969251411668
+38,9.574295991188189,1.122242688044198,0.15716352711357753,0.0184217846714555,32.035651421735295,2.574653245605423,4.104459909839981,0.32986877304942397
diff --git a/papers/scaleup/SA_optimization/data/transfer.sh b/papers/scaleup/SA_optimization/data/transfer.sh
new file mode 100644
index 00000000..870cea45
--- /dev/null
+++ b/papers/scaleup/SA_optimization/data/transfer.sh
@@ -0,0 +1,11 @@
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study/study_0_4vvm_lev1/*csv study/study_0_4vvm_lev1
+scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study/study_0_4vvm_lev2/*csv study/study_0_4vvm_lev2
+scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study/study_0_4vvm_lev3/*csv study/study_0_4vvm_lev3
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study/study_0_4vvm_lev4/*csv study/study_0_4vvm_lev4
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study/study_0_4vvm_lev5/*csv study/study_0_4vvm_lev5
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study/study_0_4vvm_lev6/*csv study/study_0_4vvm_lev6
+
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study_fine/study_0_4vvm_lev6/*csv study_fine/study_0_4vvm_lev6
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study_op/study_0_1vvm_lev6/*csv study_op/study_0_1vvm_lev6
+#scp mhassana@kestrel.hpc.nlr.gov:/scratch/mhassana/ceja_scaleup_actual/study_pbe/study_0_4vvm_lev6/*csv study_pbe/study_0_4vvm_lev6
+
diff --git a/papers/scaleup/SA_optimization/get_optimal_all_qois.py b/papers/scaleup/SA_optimization/get_optimal_all_qois.py
new file mode 100644
index 00000000..95fb6d77
--- /dev/null
+++ b/papers/scaleup/SA_optimization/get_optimal_all_qois.py
@@ -0,0 +1,436 @@
+import argparse
+import csv
+import json
+import os
+import random
+import warnings
+
+import numpy as np
+import pandas as pd
+from load_data import load_full_dataset
+from matplotlib.patches import Patch
+from model_selection import make_or_load_split, select_or_load_surrogate
+from plot_design_schematic import plot_schematic
+from prettyPlot.plotting import plt, pretty_labels, pretty_legend
+from surrogate import Surrogate_wrapper
+
+warnings.filterwarnings("ignore")
+
+QOI_COLS = {
+    "qoi": {
+        "label": r"QOI$_1$",
+        "ylabel": r"Optimal QOI$_1$ [kg$^2$/kWh$^2$]",
+    },
+    "qoi_kla": {
+        "label": r"QOI$_2$",
+        "ylabel": r"Optimal QOI$_2$ [kg$^2$/s$^2$]",
+    },
+    "qoi_sum": {
+        "label": r"QOI$_3$",
+        "ylabel": r"Optimal QOI$_3$ [kg/kWh]",
+    },
+    "qoi_sum_kla": {
+        "label": r"QOI$_4$",
+        "ylabel": r"Optimal QOI$_4$ [kg/s]",
+    },
+}
+
+
+def simulated_annealing_surrogate(
+    surrogate: Surrogate_wrapper,
+    dim: int = 11,
+    max_iters: int = 1000,
+    temp: float = 10.0,
+    alpha: float = 0.95,
+) -> tuple[np.ndarray, float, list[tuple], list[np.ndarray]]:
+    """Run SA on the surrogate and return optimal x, y, traces."""
+    x_curr = np.random.randint(0, 3, size=dim)
+    y_curr = surrogate.predict(x_curr)
+    x_best, y_best = x_curr.copy(), y_curr
+
+    trace = [(0, y_best)]
+    trace_x = [x_curr.copy()]
+
+    for i in range(max_iters):
+        x_new = x_curr.copy()
+        idx = random.randint(0, dim - 1)
+        x_new[idx] = (x_new[idx] + random.choice([-1, 1])) % 3
+        y_new = surrogate.predict(x_new)
+
+        delta = y_new - y_curr
+        if delta < 0 or np.random.rand() < np.exp(-delta / temp):
+            x_curr, y_curr = x_new, y_new
+            if y_curr < y_best:
+                x_best, y_best = x_new.copy(), y_new
+
+        trace.append((i, y_best))
+        trace_x.append(x_curr.copy())
+        temp *= alpha
+
+    return x_best, y_best, trace, trace_x
+
+
+def run_optimization(
+    X: np.ndarray,
+    y: np.ndarray,
+    model_type: str,
+    params: dict,
+    n_runs: int = 10,
+    max_iters: int = 1000,
+    bootstrap_size: int = 250,
+    out_folder: str = ".",
+    qoi_name: str = "qoi",
+    qoi_ylabel: str = "QOI",
+) -> None:
+    """Bootstrap + SA optimization for one QoI on a fixed, pre-tuned surrogate.
+
+    Hyperparameters are held fixed (``params``); each of ``n_runs`` bootstrap
+    subsets (size ``bootstrap_size``, drawn without replacement from the full
+    data) only refits the surrogate on its subset.
+    """
+    os.makedirs(out_folder, exist_ok=True)
+
+    all_x = []
+    all_y = []
+    all_traces = np.zeros((n_runs, max_iters + 1))
+    rng = np.random.default_rng(42)
+    bs = min(bootstrap_size, len(X))
+    bootstrap_idxs = [
+        rng.choice(len(X), size=bs, replace=False) for _ in range(n_runs)
+    ]
+
+    for i, idxs in enumerate(bootstrap_idxs):
+        X_sub, y_sub = X[idxs], y[idxs]
+        surrogate = Surrogate_wrapper(model_type, X_sub, y_sub, params)
+        x_best, y_best, trace, trace_x = simulated_annealing_surrogate(
+            surrogate, dim=X.shape[1], max_iters=max_iters
+        )
+
+        trace_y = [t[1] for t in trace]
+        all_traces[i, :] = trace_y
+        all_x.append(x_best)
+        all_y.append(y_best)
+
+    best_index = np.argmin(all_y)
+    best_x = all_x[best_index]
+    best_y = all_y[best_index]
+
+    df = pd.DataFrame(
+        [
+            {
+                **{f"x{j}": best_x[j] for j in range(len(best_x))},
+                "best_y": best_y,
+            }
+        ]
+    )
+    df.to_csv(
+        os.path.join(
+            out_folder,
+            f"best_bootstrap_solution_{model_type}_{qoi_name}.csv",
+        ),
+        index=False,
+    )
+    print(f"  {qoi_name} ({model_type}): best_y = {-best_y:.6g}, x = {best_x}")
+
+    # schematic of the optimum design on the reactor bottom face
+    plot_schematic(
+        best_x,
+        os.path.join(out_folder, f"Optimum_schematic_{model_type}_{qoi_name}"),
+        title=f"Optimum {qoi_name} ({model_type.upper()})",
+    )
+
+    # save the convergence-plot inputs so the plot can be regenerated later
+    # (via plot_convergence / --plot-only) without rerunning the optimization
+    np.savez(
+        _convergence_data_path(out_folder, model_type, qoi_name),
+        all_traces=all_traces,
+        qoi_lo=float((-y).min()),
+        qoi_hi=float((-y).max()),
+        best_x=np.asarray(best_x),
+        best_y=best_y,
+        all_x=np.asarray(all_x),
+        all_y=np.asarray(all_y),
+    )
+    plot_convergence(out_folder, model_type, qoi_name, qoi_ylabel)
+
+
+def _convergence_data_path(
+    out_folder: str, model_type: str, qoi_name: str
+) -> str:
+    """Path of the saved convergence-plot data for one model/QoI."""
+    return os.path.join(
+        out_folder, f"convergence_data_{model_type}_{qoi_name}.npz"
+    )
+
+
+def plot_convergence(
+    out_folder: str,
+    model_type: str,
+    qoi_name: str,
+    qoi_ylabel: str,
+) -> None:
+    """Draw the convergence plot from data saved by run_optimization.
+
+    Reads convergence_data_{model_type}_{qoi_name}.npz (the per-run SA traces
+    plus the CFD QoI range) so the plot can be regenerated without rerunning the
+    optimization. The grey band + dashed lines mark the CFD QoI range so
+    extrapolation of the optimum is easy to spot.
+    """
+    data = np.load(_convergence_data_path(out_folder, model_type, qoi_name))
+    all_traces = data["all_traces"]
+    qoi_lo = float(data["qoi_lo"])
+    qoi_hi = float(data["qoi_hi"])
+    n_runs, n_points = all_traces.shape
+    iterations = np.arange(n_points)
+
+    mean_trace = np.mean(-1 * all_traces, axis=0)
+    std_trace = np.std(all_traces, axis=0)
+    lower_bound = mean_trace - 1.96 * std_trace / np.sqrt(n_runs)
+    upper_bound = mean_trace + 1.96 * std_trace / np.sqrt(n_runs)
+
+    fig, ax = plt.subplots(figsize=(8, 6))
+    ax.axhspan(
+        qoi_lo,
+        qoi_hi,
+        color="grey",
+        alpha=0.25,
+        zorder=0,
+        label="CFD data range",
+    )
+    ax.axhline(qoi_lo, color="dimgray", ls="--", lw=1.2, zorder=5)
+    ax.axhline(qoi_hi, color="dimgray", ls="--", lw=1.2, zorder=5)
+    ax.plot(
+        iterations,
+        mean_trace,
+        label=f"Mean Convergence {model_type.upper()}",
+        color="blue",
+    )
+    ax.fill_between(
+        iterations,
+        lower_bound,
+        upper_bound,
+        color="blue",
+        alpha=0.3,
+        label="95% CI",
+    )
+    # optional red dashed line: CFD-verified QoI of an optimal design, if provided
+    cfd_file = os.path.join(out_folder, "cfd_all_spargers.txt")
+    if os.path.exists(cfd_file):
+        with open(cfd_file) as f:
+            cfd_value = float(f.read().strip().split(",")[0])
+        ax.axhline(
+            cfd_value,
+            color="red",
+            ls="--",
+            lw=3,
+            zorder=6,
+            label="All spargers",
+        )
+    pretty_labels(
+        "Iteration",
+        qoi_ylabel,
+        fontsize=30,
+        # title=f"Convergence ({model_type.upper()}, {qoi_ylabel})",
+        grid=False,
+        fontname="Times",
+    )
+    pretty_legend(fontsize=30, fontname="Times")
+    fname = f"Mean_Convergence_plot_{model_type}_{qoi_name}"
+    plt.savefig(os.path.join(out_folder, f"{fname}.png"), dpi=300)
+    plt.savefig(os.path.join(out_folder, f"{fname}.pdf"))
+    plt.close()
+
+
+# design choices shown in the bar plot: (code, bar color, name). Only spargers
+# (code 1) are shown; mixers (0) and walls (2) are omitted as less
+# physically meaningful. Order sets the bar order per QoI.
+DESIGN_CHOICES = [(1, "tab:blue", "Sparger"), (0, "tab:red", "Mixers")]
+
+
+def plot_design_composition(studies: dict, out_path: str) -> None:
+    """Bar plot of the mean sparger/mixer/wall count over the bootstrap optima.
+
+    For each (level, QoI) it reads the saved ensemble (all_x) of the winning
+    surrogate and, per placement type, plots the mean count across the bootstrap
+    optima with an error bar for the std. Blue = sparger, red = mixer,
+    grey = wall; lev1 hatched, lev6 solid. Reads only saved data, so it needs no
+    optimization rerun.
+    """
+    qoi_names = list(QOI_COLS.keys())
+    # stats[level][qoi_name][choice] = (mean_count, std_count)
+    stats = {label: {} for label in studies.values()}
+    for study_path, label in studies.items():
+        for qoi_name in qoi_names:
+            out = os.path.join(study_path, qoi_name)
+            json_path = os.path.join(out, f"hyperparams_{qoi_name}.json")
+            if not os.path.exists(json_path):
+                continue
+            with open(json_path) as f:
+                best_type = json.load(f)["best"]
+            data_path = _convergence_data_path(out, best_type, qoi_name)
+            if not os.path.exists(data_path):
+                continue
+            npz = np.load(data_path)
+            if "all_x" not in npz.files:
+                print(
+                    f"  {label}/{qoi_name}: npz has no all_x (rerun to save)"
+                )
+                continue
+            all_x = npz["all_x"]
+            stats[label][qoi_name] = {
+                choice: (
+                    float((all_x == choice).sum(axis=1).mean()),
+                    float((all_x == choice).sum(axis=1).std()),
+                )
+                for choice, _, _ in DESIGN_CHOICES
+            }
+
+    ordered_levels = sorted(studies.values())  # lev1 (hatched) before lev6
+    n_bars = len(DESIGN_CHOICES) * len(ordered_levels)
+    bar_width = 0.8 / n_bars
+    x_ticks = np.arange(len(qoi_names))
+
+    fig, ax = plt.subplots(figsize=(11, 6))
+    slot = 0
+    for choice, color, _ in DESIGN_CHOICES:
+        for level in ordered_levels:
+            means = [
+                stats[level].get(q, {}).get(choice, (np.nan, np.nan))[0]
+                for q in qoi_names
+            ]
+            stds = [
+                stats[level].get(q, {}).get(choice, (np.nan, np.nan))[1]
+                for q in qoi_names
+            ]
+            offset = (slot - (n_bars - 1) / 2) * bar_width
+            ax.bar(
+                x_ticks + offset,
+                means,
+                bar_width,
+                yerr=stds,
+                capsize=3,
+                color=color,
+                edgecolor="black",
+                hatch="//" if level == "lev1" else None,
+            )
+            slot += 1
+
+    pretty_labels(
+        "",
+        "Average count over bootstrap optima",
+        fontsize=20,
+        grid=True,
+        fontname="Times",
+    )
+    ax.set_xticks(x_ticks)
+    ax.set_xticklabels([QOI_COLS[q]["label"] for q in qoi_names])
+    legend_handles = [
+        Patch(facecolor=color, edgecolor="black", label=name)
+        for _, color, name in DESIGN_CHOICES
+    ] + [
+        Patch(facecolor="white", edgecolor="black", hatch="//", label="3.6L"),
+        Patch(facecolor="white", edgecolor="black", label=r"608 m$^3$"),
+    ]
+    ax.legend(handles=legend_handles, fontsize=14)
+    plt.savefig(f"{out_path}.png", dpi=300)
+    plt.savefig(f"{out_path}.pdf")
+    plt.close()
+
+
+if __name__ == "__main__":
+    studies = {
+        "data/study/study_0_4vvm_lev6": "lev6",
+        "data/study/study_0_4vvm_lev1": "lev1",
+    }
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--plot-only",
+        action="store_true",
+        help="skip the optimization and regenerate the convergence plots from "
+        "the saved convergence_data_*.npz in each qoi folder",
+    )
+    args = parser.parse_args()
+
+    selection_rows = []
+    for study_path, label in studies.items():
+        print(f"\n=== {label}: {study_path} ===")
+        if not args.plot_only:
+            X, Y_full = load_full_dataset(study_path)
+            split = make_or_load_split(
+                study_path, n_samples=len(X), n_test=20, n_val=20
+            )
+
+        for qoi_name, qoi_info in QOI_COLS.items():
+            out = os.path.join(study_path, qoi_name)
+            json_path = os.path.join(out, f"hyperparams_{qoi_name}.json")
+
+            if args.plot_only:
+                if not os.path.exists(json_path):
+                    print(f"  skip {qoi_name}: no {json_path} (run first)")
+                    continue
+                with open(json_path) as f:
+                    record = json.load(f)
+                best_type = record["best"]
+                if not os.path.exists(
+                    _convergence_data_path(out, best_type, qoi_name)
+                ):
+                    print(f"  skip {qoi_name}: no saved convergence data")
+                    continue
+                plot_convergence(out, best_type, qoi_name, qoi_info["ylabel"])
+                print(f"  {qoi_name}: replotted ({best_type})")
+            else:
+                y = Y_full[qoi_name].values.reshape(-1, 1) * -1
+                best_type, best_params = select_or_load_surrogate(
+                    X, y, split, qoi_name, out
+                )
+                with open(json_path) as f:
+                    record = json.load(f)
+                run_optimization(
+                    X,
+                    y,
+                    model_type=best_type,
+                    params=best_params,
+                    n_runs=50,
+                    max_iters=1000,
+                    bootstrap_size=250,
+                    out_folder=out,
+                    qoi_name=qoi_name,
+                    qoi_ylabel=qoi_info["ylabel"],
+                )
+
+            selection_rows.append(
+                {
+                    "level": label,
+                    "qoi_name": qoi_name,
+                    "best": best_type,
+                    "val_mse": record[best_type]["val_mse"],
+                    "val_nrmse_amp_pct": record[best_type][
+                        "val_nrmse_amp_pct"
+                    ],
+                    "val_nrmse_mean_pct": record[best_type][
+                        "val_nrmse_mean_pct"
+                    ],
+                    "best_params": record["best_params"],
+                }
+            )
+
+    with open("surrogate_selection.csv", "w", newline="") as f:
+        writer = csv.DictWriter(
+            f,
+            fieldnames=[
+                "level",
+                "qoi_name",
+                "best",
+                "val_mse",
+                "val_nrmse_amp_pct",
+                "val_nrmse_mean_pct",
+                "best_params",
+            ],
+        )
+        writer.writeheader()
+        writer.writerows(selection_rows)
+    print("\nWrote surrogate_selection.csv")
+
+    plot_design_composition(studies, "design_composition_barplot")
+    print("Wrote design_composition_barplot.png")
diff --git a/papers/scaleup/SA_optimization/get_optimal_constrained.py b/papers/scaleup/SA_optimization/get_optimal_constrained.py
new file mode 100644
index 00000000..c0fc81c1
--- /dev/null
+++ b/papers/scaleup/SA_optimization/get_optimal_constrained.py
@@ -0,0 +1,175 @@
+import csv
+import os
+import random
+import warnings
+
+import numpy as np
+from load_data import load_full_dataset
+from model_selection import make_or_load_split, select_or_load_surrogate
+from surrogate import Surrogate_wrapper
+
+warnings.filterwarnings("ignore")
+
+QOI_COLS = {
+    "qoi": {"label": "QOI"},
+    "qoi_kla": {"label": "QOI Num"},
+    "qoi_sum": {"label": "QOI Sum"},
+    "qoi_sum_kla": {"label": "QOI Sum Num"},
+}
+
+
+def simulated_annealing_constrained(
+    surrogate: Surrogate_wrapper,
+    dim: int = 11,
+    max_iters: int = 1000,
+    max_spargers: int = 8,
+    temp: float = 10.0,
+    alpha: float = 0.95,
+) -> tuple[np.ndarray, float, list[tuple]]:
+    """SA constrained by max number of spargers."""
+
+    def is_valid(x):
+        return np.sum(x == 1) <= max_spargers
+
+    while True:
+        x_curr = np.random.randint(0, 3, size=dim)
+        if is_valid(x_curr):
+            break
+
+    y_curr = surrogate.predict(x_curr)
+    x_best, y_best = x_curr.copy(), y_curr
+    trace = [(0, y_best)]
+
+    for i in range(max_iters):
+        x_new = x_curr.copy()
+        idx = random.randint(0, dim - 1)
+        x_new[idx] = (x_new[idx] + random.choice([-1, 1])) % 3
+
+        if not is_valid(x_new):
+            trace.append((i, y_best))
+            temp *= alpha
+            continue
+
+        y_new = surrogate.predict(x_new)
+        delta = y_new - y_curr
+        if delta < 0 or np.random.rand() < np.exp(-delta / temp):
+            x_curr, y_curr = x_new, y_new
+            if y_curr < y_best:
+                x_best, y_best = x_new.copy(), y_new
+
+        trace.append((i, y_best))
+        temp *= alpha
+
+    return x_best, y_best, trace
+
+
+def run_constrained_optimization(
+    X: np.ndarray,
+    y: np.ndarray,
+    model_type: str,
+    params: dict,
+    max_spargers: int = 8,
+    n_runs: int = 10,
+    max_iters: int = 1000,
+    bootstrap_size: int = 250,
+) -> tuple[float, float]:
+    """Mean optimal QoI over the bootstrap optima and its 95% uncertainty.
+
+    Each bootstrap subset refits the fixed, pre-tuned surrogate
+    (``model_type`` + ``params``) and yields one constrained optimum. Returns
+    the mean of those optima (positive, i.e. negated back to physical) and the
+    95% confidence interval of that mean (1.96 * std / sqrt(n_runs)).
+    """
+    rng = np.random.default_rng(42)
+    bs = min(bootstrap_size, len(X))
+    bootstrap_idxs = [
+        rng.choice(len(X), size=bs, replace=False) for _ in range(n_runs)
+    ]
+
+    all_y = []
+    for idxs in bootstrap_idxs:
+        X_sub, y_sub = X[idxs], y[idxs]
+        surrogate = Surrogate_wrapper(model_type, X_sub, y_sub, params)
+        _, y_best, _ = simulated_annealing_constrained(
+            surrogate,
+            dim=X.shape[1],
+            max_iters=max_iters,
+            max_spargers=max_spargers,
+        )
+        all_y.append(y_best)
+
+    optima = -np.array(all_y)  # negate back to physical QoI
+    mean_optimum = float(np.mean(optima))
+    ci95 = float(1.96 * np.std(optima) / np.sqrt(len(optima)))
+    return mean_optimum, ci95
+
+
+if __name__ == "__main__":
+    studies = {
+        "data/study/study_0_4vvm_lev1": "lev1",
+        "data/study/study_0_4vvm_lev6": "lev6",
+    }
+
+    results = []
+
+    for study_path, level_label in studies.items():
+        print(f"\n=== {level_label}: {study_path} ===")
+        X, Y_full = load_full_dataset(study_path)
+
+        split = make_or_load_split(
+            study_path, n_samples=len(X), n_test=20, n_val=20
+        )
+
+        for qoi_name, qoi_info in QOI_COLS.items():
+            y = Y_full[qoi_name].values.reshape(-1, 1) * -1
+
+            # winning surrogate + tuned params (cached from the selection step)
+            out = os.path.join(study_path, qoi_name)
+            model_type, params = select_or_load_surrogate(
+                X, y, split, qoi_name, out
+            )
+
+            for nsparg in range(3, 10):
+                print(
+                    f"  {qoi_name} ({model_type}), max_spargers={nsparg}...",
+                    end="",
+                    flush=True,
+                )
+                mean_optimum, ci95 = run_constrained_optimization(
+                    X,
+                    y,
+                    model_type=model_type,
+                    params=params,
+                    max_spargers=nsparg,
+                    n_runs=10,
+                    max_iters=1000,
+                    bootstrap_size=250,
+                )
+                print(f" mean={mean_optimum:.6g} ci95={ci95:.6g}")
+                results.append(
+                    {
+                        "level": level_label,
+                        "qoi_name": qoi_name,
+                        "model_type": model_type,
+                        "n_spargers": nsparg,
+                        "optimal_qoi_mean": mean_optimum,
+                        "optimal_qoi_ci95": ci95,
+                    }
+                )
+
+    out_file = "marginal_gain_results.csv"
+    with open(out_file, "w", newline="") as f:
+        writer = csv.DictWriter(
+            f,
+            fieldnames=[
+                "level",
+                "qoi_name",
+                "model_type",
+                "n_spargers",
+                "optimal_qoi_mean",
+                "optimal_qoi_ci95",
+            ],
+        )
+        writer.writeheader()
+        writer.writerows(results)
+    print(f"\nWrote {out_file}")
diff --git a/papers/scaleup/SA_optimization/load_data.py b/papers/scaleup/SA_optimization/load_data.py
new file mode 100644
index 00000000..244cde68
--- /dev/null
+++ b/papers/scaleup/SA_optimization/load_data.py
@@ -0,0 +1,45 @@
+import os
+
+import numpy as np
+import pandas as pd
+
+# the 4 QoI value columns the surrogate can target (each has a matching _err)
+QOI_VALUE_COLS = ["qoi", "qoi_kla", "qoi_sum", "qoi_sum_kla"]
+QOI_ERR_COLS = ["qoi_err", "qoi_kla_err", "qoi_sum_err", "qoi_sum_kla_err"]
+
+# QoI assigned to unreliable designs, and the SNR gate for "reliable"
+FAILED_QOI_VALUE = 0.0
+SNR_THRESHOLD = 5.0
+
+
+def _is_reliable(value: float, err: float, threshold: float) -> bool:
+    """True when the signal-to-noise ratio |value| / err meets the threshold."""
+    return err > 0 and abs(value) / err >= threshold
+
+
+def load_full_dataset(study_path: str) -> tuple[np.ndarray, pd.DataFrame]:
+    converged_X = pd.read_csv(
+        os.path.join(study_path, "X_data.csv"), header=None
+    ).values
+    converged_Y = pd.read_csv(os.path.join(study_path, "Y_data.csv"))
+
+    X = converged_X.astype(int)
+    Y_rows = []
+    for row_index in range(len(converged_Y)):
+        source = converged_Y.iloc[row_index]
+        row = {"sim_id": int(source["sim_id"])}
+        for qoi, err_col in zip(QOI_VALUE_COLS, QOI_ERR_COLS):
+            value = float(source[qoi])
+            err = float(source[err_col])
+            row[qoi] = (
+                value
+                if _is_reliable(value, err, SNR_THRESHOLD)
+                else FAILED_QOI_VALUE
+            )
+            row[err_col] = err
+        Y_rows.append(row)
+
+    column_order = ["sim_id"] + QOI_VALUE_COLS + QOI_ERR_COLS
+    Y = pd.DataFrame(Y_rows)[column_order].reset_index(drop=True)
+    Y["sim_id"] = Y["sim_id"].astype(int)
+    return X, Y
diff --git a/papers/scaleup/SA_optimization/make_hyperparam_tables.py b/papers/scaleup/SA_optimization/make_hyperparam_tables.py
new file mode 100644
index 00000000..8afbc06d
--- /dev/null
+++ b/papers/scaleup/SA_optimization/make_hyperparam_tables.py
@@ -0,0 +1,158 @@
+import json
+from pathlib import Path
+from typing import Callable
+
+SCRIPT_DIR = Path(__file__).parent
+STUDY_DIR = SCRIPT_DIR / "data" / "study"
+
+# QoI key -> LaTeX row label. Order matches QOI_COLS in get_optimal_all_qois.py.
+QOI_LABELS = {
+    "qoi": r"$\rm{QOI}_1 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+    "qoi_kla": r"$\rm{QOI}_2 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+    "qoi_sum": r"$\rm{QOI}_3 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+    "qoi_sum_kla": r"$\rm{QOI}_4 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+}
+
+# Surrogate label -> key inside the hyperparams JSON.
+SURROGATE_COLUMNS = {"RBF": "rbf", "RF": "rf", "MLP": "nn"}
+
+LEVELS = ("lev1", "lev6")
+
+
+def format_int(value: float) -> str:
+    return str(int(value))
+
+
+def format_float(value: float) -> str:
+    """3 significant figures; scientific notation rewritten to LaTeX math."""
+    text = f"{value:.3g}"
+    if "e" in text:
+        mantissa, exponent = text.split("e")
+        return rf"{mantissa}\times10^{{{int(exponent)}}}"
+    return text
+
+
+def format_kernel(value: str) -> str:
+    return rf"\texttt{{{value.replace('_', r'\_')}}}"
+
+
+# Per-surrogate column spec: (json param key, LaTeX header, formatter, is_math).
+Formatter = Callable[[object], str]
+SURROGATE_PARAMS: dict[str, list[tuple[str, str, Formatter, bool]]] = {
+    "RBF": [
+        ("epsilon", r"$\epsilon$", format_float, True),
+        ("kernel", "Kernel", format_kernel, False),
+    ],
+    "RF": [
+        ("n_estimators", r"$n_{\rm trees}$", format_int, True),
+        ("max_depth", "depth", format_int, True),
+        ("min_samples_leaf", "min. leaf", format_int, True),
+        ("max_features", "max. feat.", format_float, True),
+    ],
+    "MLP": [
+        ("n_units", "units", format_int, True),
+        ("n_layers", "layers", format_int, True),
+        ("lr", "lr", format_float, True),
+    ],
+}
+
+
+def read_params(level: str, qoi_key: str, model_key: str) -> dict:
+    """Optimal hyperparameters for one level/QoI/surrogate."""
+    json_path = (
+        STUDY_DIR
+        / f"study_0_4vvm_{level}"
+        / qoi_key
+        / f"hyperparams_{qoi_key}.json"
+    )
+    with open(json_path) as json_file:
+        hyperparams = json.load(json_file)
+    return hyperparams[model_key]["params"]
+
+
+def build_cell(lev1_text: str, lev6_text: str, is_math: bool) -> str:
+    inner = f"{lev1_text} / {lev6_text}"
+    body = f"${inner}$" if is_math else inner
+    return rf"\rev{{{body}}}"
+
+
+def build_table(surrogate_label: str) -> str:
+    model_key = SURROGATE_COLUMNS[surrogate_label]
+    columns = SURROGATE_PARAMS[surrogate_label]
+    headers = [header for _, header, _, _ in columns]
+
+    lines = [
+        r"\begin{table}[h]",
+        r"\centering",
+        r"\begin{tabular}{ |l|" + "c|" * len(headers) + " }",
+        r"\hline",
+        r"\rev{QoI} & "
+        + " & ".join(rf"\rev{{{header}}}" for header in headers)
+        + r" \\",
+        r"\hline",
+    ]
+
+    for qoi_key, row_label in QOI_LABELS.items():
+        lev1_params = read_params("lev1", qoi_key, model_key)
+        lev6_params = read_params("lev6", qoi_key, model_key)
+        cells = [
+            build_cell(
+                formatter(lev1_params[param_key]),
+                formatter(lev6_params[param_key]),
+                is_math,
+            )
+            for param_key, _, formatter, is_math in columns
+        ]
+        lines.append(
+            rf"\rev{{{row_label}}} & " + " & ".join(cells) + r" \\ \hline"
+        )
+
+    lines += [
+        r"\end{tabular}",
+        rf"\caption{{\rev{{Optimal {surrogate_label} hyperparameters for "
+        r"each QoI, at reactor scales $3.6\,$L (lev1) $/$ $608\,$m$^3$ "
+        r"(lev6).}}",
+        rf"\label{{tab:hyperparams_{model_key}}}",
+        r"\end{table}",
+    ]
+    return "\n".join(lines)
+
+
+def write_wrapper(table_file_names: list[str], out_path: Path) -> None:
+    """Standalone document that defines \\rev (red) and inputs each table."""
+    inputs = [rf"\input{{{name}}}" for name in table_file_names]
+    wrapper = "\n".join(
+        [
+            r"\documentclass{article}",
+            r"\usepackage[margin=1in]{geometry}",
+            r"\usepackage{xcolor}",
+            r"\newcommand{\rev}[1]{\textcolor{red}{#1}}",
+            r"\begin{document}",
+            *inputs,
+            r"\end{document}",
+        ]
+    )
+    with open(out_path, "w") as wrapper_file:
+        wrapper_file.write(wrapper)
+    print(f"Wrote {out_path}")
+
+
+def main() -> None:
+    table_file_names = []
+    for surrogate_label, model_key in SURROGATE_COLUMNS.items():
+        table = build_table(surrogate_label)
+        print(table)
+        print()
+
+        table_file_name = f"hyperparams_{model_key}_table.tex"
+        table_path = SCRIPT_DIR / table_file_name
+        with open(table_path, "w") as table_file:
+            table_file.write(table)
+        print(f"Wrote {table_path}")
+        table_file_names.append(table_file_name)
+
+    write_wrapper(table_file_names, SCRIPT_DIR / "view_hyperparam_tables.tex")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/papers/scaleup/SA_optimization/make_val_rmse_table.py b/papers/scaleup/SA_optimization/make_val_rmse_table.py
new file mode 100644
index 00000000..f1d630ef
--- /dev/null
+++ b/papers/scaleup/SA_optimization/make_val_rmse_table.py
@@ -0,0 +1,117 @@
+import json
+from pathlib import Path
+
+SCRIPT_DIR = Path(__file__).parent
+STUDY_DIR = SCRIPT_DIR / "data" / "study"
+
+# QoI key -> LaTeX row label. Order matches QOI_COLS in get_optimal_all_qois.py.
+QOI_LABELS = {
+    "qoi": r"$\rm{QOI}_1 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+    "qoi_kla": r"$\rm{QOI}_2 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+    "qoi_sum": r"$\rm{QOI}_3 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+    "qoi_sum_kla": r"$\rm{QOI}_4 (3.6\, \rm{L}~/~608\, \rm{m}^3)$",
+}
+
+# Surrogate column header -> key inside the hyperparams JSON.
+SURROGATE_COLUMNS = {"RBF": "rbf", "RF": "rf", "MLP": "nn"}
+
+LEVELS = ("lev1", "lev6")
+METRIC_KEY = "val_nrmse_amp_pct"
+
+
+def read_val_nrmse(level: str, qoi_key: str) -> dict[str, float]:
+    """Validation nRMSE (% of amplitude) for each surrogate at one level/QoI."""
+    json_path = (
+        STUDY_DIR
+        / f"study_0_4vvm_{level}"
+        / qoi_key
+        / f"hyperparams_{qoi_key}.json"
+    )
+    with open(json_path) as json_file:
+        hyperparams = json.load(json_file)
+    return {
+        column: float(hyperparams[model_key][METRIC_KEY])
+        for column, model_key in SURROGATE_COLUMNS.items()
+    }
+
+
+def format_number(value: float, is_lowest: bool) -> str:
+    text = f"{value:.1f}"
+    return rf"\textbf{{{text}}}" if is_lowest else text
+
+
+def build_cell(
+    lev1_value: float,
+    lev6_value: float,
+    lev1_is_lowest: bool,
+    lev6_is_lowest: bool,
+) -> str:
+    lev1_text = format_number(lev1_value, lev1_is_lowest)
+    lev6_text = format_number(lev6_value, lev6_is_lowest)
+    return rf"${lev1_text}\% / {lev6_text}\%$"
+
+
+def build_table() -> str:
+    column_headers = list(SURROGATE_COLUMNS)
+    lines = [
+        r"\begin{tabular}{l" + "c" * len(column_headers) + "}",
+        r"\hline",
+        "QoI & " + " & ".join(column_headers) + r" \\",
+        r"\hline",
+    ]
+
+    for qoi_key, row_label in QOI_LABELS.items():
+        lev1_values = read_val_nrmse("lev1", qoi_key)
+        lev6_values = read_val_nrmse("lev6", qoi_key)
+        lev1_lowest_column = min(lev1_values, key=lev1_values.get)
+        lev6_lowest_column = min(lev6_values, key=lev6_values.get)
+
+        cells = [
+            build_cell(
+                lev1_values[column],
+                lev6_values[column],
+                column == lev1_lowest_column,
+                column == lev6_lowest_column,
+            )
+            for column in column_headers
+        ]
+        lines.append(f"{row_label} & " + " & ".join(cells) + r" \\")
+
+    lines += [r"\hline", r"\end{tabular}"]
+    return "\n".join(lines)
+
+
+def write_wrapper(table_file_name: str, out_path: Path) -> None:
+    wrapper = "\n".join(
+        [
+            r"\documentclass{article}",
+            r"\usepackage[margin=1in]{geometry}",
+            r"\begin{document}",
+            r"\begin{table}[h]",
+            r"\centering",
+            rf"\input{{{table_file_name}}}",
+            r"\caption{Validation nRMSE relative to amplitude "
+            r"(lev1 $3.6\,$L / lev6 $608\,$m$^3$); lowest per level in bold.}",
+            r"\end{table}",
+            r"\end{document}",
+        ]
+    )
+    with open(out_path, "w") as wrapper_file:
+        wrapper_file.write(wrapper)
+    print(f"Wrote {out_path}")
+
+
+def main() -> None:
+    table = build_table()
+    print(table)
+
+    table_path = SCRIPT_DIR / "val_rmse_table.tex"
+    with open(table_path, "w") as table_file:
+        table_file.write(table)
+    print(f"Wrote {table_path}")
+
+    write_wrapper("val_rmse_table.tex", SCRIPT_DIR / "view_val_rmse_table.tex")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/papers/scaleup/SA_optimization/marginal_gain_results.csv b/papers/scaleup/SA_optimization/marginal_gain_results.csv
new file mode 100644
index 00000000..9723e371
--- /dev/null
+++ b/papers/scaleup/SA_optimization/marginal_gain_results.csv
@@ -0,0 +1,57 @@
+level,qoi_name,model_type,n_spargers,optimal_qoi_mean,optimal_qoi_ci95
+lev1,qoi,nn,3,20.777002658440317,4.967135709603668
+lev1,qoi,nn,4,29.33137591333509,6.052693630554447
+lev1,qoi,nn,5,28.728691798440696,7.782960094406028
+lev1,qoi,nn,6,28.00670375941676,5.250816613929773
+lev1,qoi,nn,7,26.578156696520818,6.211729307089006
+lev1,qoi,nn,8,25.752087994106507,5.750639405478412
+lev1,qoi,nn,9,33.39666583737389,6.095517715388951
+lev1,qoi_kla,nn,3,2.1630368613455053e-12,5.646098656009841e-13
+lev1,qoi_kla,nn,4,2.1810997777515023e-12,7.571885282140608e-13
+lev1,qoi_kla,nn,5,2.2262035694651713e-12,7.283823393852845e-13
+lev1,qoi_kla,nn,6,1.919642208364238e-12,7.524940381917437e-13
+lev1,qoi_kla,nn,7,2.270919638464332e-12,6.688943592320943e-13
+lev1,qoi_kla,nn,8,2.1171600394206276e-12,7.240310078697636e-13
+lev1,qoi_kla,nn,9,2.704915189390905e-12,8.320571300855766e-13
+lev1,qoi_sum,nn,3,34.330421521427105,1.5979910200579341
+lev1,qoi_sum,nn,4,36.93759964547867,2.6326362889827815
+lev1,qoi_sum,nn,5,37.37891391484199,1.9716201424039503
+lev1,qoi_sum,nn,6,37.88222566926674,2.0477026431202336
+lev1,qoi_sum,nn,7,38.30321346647001,1.5016840895363077
+lev1,qoi_sum,nn,8,38.52937161920444,1.9463582167721076
+lev1,qoi_sum,nn,9,38.44378376449916,2.5630231918745983
+lev1,qoi_sum_kla,nn,3,7.804334100887237e-06,1.3813566415684952e-07
+lev1,qoi_sum_kla,nn,4,7.8251175178686e-06,1.1370595131964046e-07
+lev1,qoi_sum_kla,nn,5,7.734468577471196e-06,2.8786262283158653e-07
+lev1,qoi_sum_kla,nn,6,7.827537738907247e-06,1.5470669237093723e-07
+lev1,qoi_sum_kla,nn,7,7.704540831548307e-06,2.2034748906434659e-07
+lev1,qoi_sum_kla,nn,8,7.739101235354367e-06,2.6253140249004177e-07
+lev1,qoi_sum_kla,nn,9,7.619820316451526e-06,3.25479214629696e-07
+lev6,qoi,nn,3,15.909415092123254,0.46775342270960824
+lev6,qoi,nn,4,17.479575262616905,0.8682770294330613
+lev6,qoi,nn,5,18.754729256260596,0.529543994336786
+lev6,qoi,nn,6,19.886590714439063,0.3755539258889765
+lev6,qoi,nn,7,21.433241721384228,0.5610737501452722
+lev6,qoi,nn,8,21.610978671926706,1.0828448639168482
+lev6,qoi,nn,9,20.93777004972596,1.9637920266145474
+lev6,qoi_kla,nn,3,0.24658579471534098,0.008536403046175908
+lev6,qoi_kla,nn,4,0.27306325796051867,0.0057937584699469255
+lev6,qoi_kla,nn,5,0.2941745217305499,0.00715797413420681
+lev6,qoi_kla,nn,6,0.30658919100619186,0.00623891361279496
+lev6,qoi_kla,nn,7,0.31463449818349964,0.005752463990180858
+lev6,qoi_kla,nn,8,0.3187942689999229,0.008043733761107999
+lev6,qoi_kla,nn,9,0.33383378816617665,0.007553545891181331
+lev6,qoi_sum,nn,3,37.37678159715111,0.7814896878666623
+lev6,qoi_sum,nn,4,38.04317682799514,0.6625226569542539
+lev6,qoi_sum,nn,5,39.5093564959566,0.9260206104420369
+lev6,qoi_sum,nn,6,39.70000734500967,0.592021708828062
+lev6,qoi_sum,nn,7,39.07709702857392,0.4739951040219765
+lev6,qoi_sum,nn,8,39.57371845662897,0.18470348275441084
+lev6,qoi_sum,nn,9,39.844698183642166,0.3826178119788762
+lev6,qoi_sum_kla,rbf,3,4.830869504994335,0.10543249459025254
+lev6,qoi_sum_kla,rbf,4,4.966668120244677,0.15220367538664611
+lev6,qoi_sum_kla,rbf,5,5.111496616028076,0.07325606131503833
+lev6,qoi_sum_kla,rbf,6,5.182008623639471,0.0704755723932477
+lev6,qoi_sum_kla,rbf,7,5.161792010502566,0.08237835929861465
+lev6,qoi_sum_kla,rbf,8,5.252289373978056,0.04793709953939311
+lev6,qoi_sum_kla,rbf,9,5.233795924095803,0.04269007121971121
diff --git a/papers/scaleup/SA_optimization/model_selection.py b/papers/scaleup/SA_optimization/model_selection.py
new file mode 100644
index 00000000..a44ba125
--- /dev/null
+++ b/papers/scaleup/SA_optimization/model_selection.py
@@ -0,0 +1,139 @@
+import json
+import os
+
+import numpy as np
+import pandas as pd
+from sklearn.metrics import mean_squared_error
+from surrogate import Surrogate_wrapper, tune_nn, tune_rbf, tune_rf
+
+
+def make_or_load_split(
+    study_path: str,
+    n_samples: int,
+    n_test: int = 20,
+    n_val: int = 20,
+    seed: int = 0,
+) -> dict:
+    """Return {'train','test','val'} row-index arrays, frozen in split.csv.
+
+    If split.csv already exists in ``study_path`` it is loaded verbatim so the
+    split is reproducible across runs; otherwise it is drawn deterministically
+    from ``seed`` and written.
+    """
+    split_file = os.path.join(study_path, "split.csv")
+    if os.path.exists(split_file):
+        df = pd.read_csv(split_file)
+        return {
+            name: df.loc[df["set"] == name, "row_index"].to_numpy()
+            for name in ("train", "test", "val")
+        }
+
+    rng = np.random.default_rng(seed)
+    perm = rng.permutation(n_samples)
+    test_idx = perm[:n_test]
+    val_idx = perm[n_test : n_test + n_val]
+    train_idx = perm[n_test + n_val :]
+
+    rows = (
+        [(int(i), "test") for i in test_idx]
+        + [(int(i), "val") for i in val_idx]
+        + [(int(i), "train") for i in train_idx]
+    )
+    pd.DataFrame(rows, columns=["row_index", "set"]).to_csv(
+        split_file, index=False
+    )
+    return {"train": train_idx, "test": test_idx, "val": val_idx}
+
+
+def _predict_batch(surrogate: Surrogate_wrapper, X: np.ndarray) -> np.ndarray:
+    """Row-wise predictions (Surrogate_wrapper.predict is single-sample)."""
+    return np.array([surrogate.predict(X[i]) for i in range(len(X))])
+
+
+def select_or_load_surrogate(
+    X: np.ndarray,
+    y: np.ndarray,
+    split: dict,
+    qoi_name: str,
+    out_folder: str,
+    n_trials: int = 100,
+) -> tuple[str, dict]:
+    """Tune RBF, RF, and NN on the test set, pick the winner on the validation set.
+
+    Caches the full result to ``hyperparams_{qoi_name}.json`` and reloads it on
+    subsequent calls so both drivers reuse one selection. Returns
+    ``(best_model_type, best_params)``.
+    """
+    os.makedirs(out_folder, exist_ok=True)
+    json_file = os.path.join(out_folder, f"hyperparams_{qoi_name}.json")
+    if os.path.exists(json_file):
+        with open(json_file) as f:
+            record = json.load(f)
+        return record["best"], record["best_params"]
+
+    X_train, y_train = X[split["train"]], y[split["train"]]
+    X_test, y_test = X[split["test"]], y[split["test"]]
+    X_val, y_val = X[split["val"]], y[split["val"]]
+
+    # physical QoI reference values (y is the negated min-space target, so
+    # physical QoI = -y). Amplitude = max - min = the CFD data range height.
+    physical = -y
+    amp_physical = float(np.max(physical) - np.min(physical))
+    mean_physical = float(np.mean(physical))
+
+    def nrmse_pct(mse: float, denom: float) -> float:
+        """Normalized RMSE as a percent of a physical-QoI reference."""
+        if denom == 0:
+            return float("nan")
+        return 100.0 * np.sqrt(mse) / abs(denom)
+
+    # 1. HPO scored on the test set
+    tuners = {"rbf": tune_rbf, "rf": tune_rf, "nn": tune_nn}
+    tuned = {
+        name: tuner(X_train, y_train, X_test, y_test, n_trials=n_trials)
+        for name, tuner in tuners.items()
+    }
+
+    # 2. compare on the validation set (each refit on the train pool). MSE is in
+    # physical units since Surrogate_wrapper.predict inverse-transforms.
+    results = {}
+    for model_type, params in tuned.items():
+        surrogate = Surrogate_wrapper(model_type, X_train, y_train, params)
+        test_mse = mean_squared_error(
+            y_test.ravel(), _predict_batch(surrogate, X_test)
+        )
+        val_mse = mean_squared_error(
+            y_val.ravel(), _predict_batch(surrogate, X_val)
+        )
+        results[model_type] = {
+            "params": params,
+            "test_mse": float(test_mse),
+            "val_mse": float(val_mse),
+            "test_nrmse_amp_pct": float(nrmse_pct(test_mse, amp_physical)),
+            "test_nrmse_mean_pct": float(nrmse_pct(test_mse, mean_physical)),
+            "val_nrmse_amp_pct": float(nrmse_pct(val_mse, amp_physical)),
+            "val_nrmse_mean_pct": float(nrmse_pct(val_mse, mean_physical)),
+        }
+
+    best = min(results, key=lambda m: results[m]["val_mse"])
+    record = {
+        "qoi": qoi_name,
+        "best": best,
+        "best_params": results[best]["params"],
+        "amp_physical": amp_physical,
+        "mean_physical": mean_physical,
+        **results,
+    }
+    with open(json_file, "w") as f:
+        json.dump(record, f, indent=2)
+
+    val_summary = ", ".join(
+        f"{m.upper()} val_mse={results[m]['val_mse']:.6g}"
+        f" (nRMSE amp={results[m]['val_nrmse_amp_pct']:.1f}%"
+        f" mean={results[m]['val_nrmse_mean_pct']:.1f}%)"
+        for m in results
+    )
+    print(f"  {qoi_name}: {val_summary} -> best={best}")
+    for m in results:
+        print(f"    {m.upper()} params: {results[m]['params']}")
+    return best, results[best]["params"]
diff --git a/papers/scaleup/SA_optimization/plot_design_schematic.py b/papers/scaleup/SA_optimization/plot_design_schematic.py
new file mode 100644
index 00000000..60677ac6
--- /dev/null
+++ b/papers/scaleup/SA_optimization/plot_design_schematic.py
@@ -0,0 +1,121 @@
+import argparse
+
+import numpy as np
+import pandas as pd
+from matplotlib.lines import Line2D
+from matplotlib.patches import Circle
+from prettyPlot.plotting import plt
+
+# fraction-along-branch of each spot (matches randsim.optimization_setup)
+BRANCH_SPOTS = {
+    0: np.linspace(0.2, 0.8, 4),
+    1: np.linspace(0.2, 0.8, 3),
+    2: np.linspace(0.2, 0.8, 4),
+}
+
+# bottom-face leg endpoints in (x, z) block coords (matches mesh.json Fluids)
+BRANCH_ENDS = {
+    0: ((0.0, 0.0), (9.0, 0.0)),
+    1: ((9.0, 0.0), (9.0, 4.0)),
+    2: ((9.0, 4.0), (0.0, 4.0)),
+}
+
+CHOICE_COLOR = {1: "tab:blue", 0: "red", 2: "black"}
+CHOICE_NAME = {1: "Sparger", 0: "Mixer", 2: "Wall"}
+
+
+def spot_positions() -> list[tuple[float, float]]:
+    """(x, z) of the 11 spots, ordered as the design vector [b0, b1, b2]."""
+    positions = []
+    for branch_id in (0, 1, 2):
+        (start_x, start_z), (end_x, end_z) = BRANCH_ENDS[branch_id]
+        for frac in BRANCH_SPOTS[branch_id]:
+            positions.append(
+                (
+                    start_x + frac * (end_x - start_x),
+                    start_z + frac * (end_z - start_z),
+                )
+            )
+    return positions
+
+
+def plot_schematic(
+    design_x: np.ndarray, out_path: str, title: str | None = None
+) -> None:
+    """Draw the bottom-face schematic for one design vector (length 11)."""
+    design_x = np.asarray(design_x, dtype=int)
+    if len(design_x) != 11:
+        raise ValueError(f"expected 11 design values, got {len(design_x)}")
+    positions = spot_positions()
+
+    fig, ax = plt.subplots(figsize=(7, 4))
+    # legs as thick rounded grey lines (the tube centerlines)
+    for branch_id in (0, 1, 2):
+        (start_x, start_z), (end_x, end_z) = BRANCH_ENDS[branch_id]
+        ax.plot(
+            [start_x, end_x],
+            [start_z, end_z],
+            color="lightgray",
+            linewidth=16,
+            solid_capstyle="round",
+            zorder=1,
+        )
+    # placement spots
+    for (spot_x, spot_z), choice in zip(positions, design_x):
+        ax.add_patch(
+            Circle(
+                (spot_x, spot_z),
+                0.32,
+                facecolor=CHOICE_COLOR[int(choice)],
+                edgecolor="k",
+                linewidth=1.2,
+                zorder=3,
+            )
+        )
+
+    ax.set_aspect("equal")
+    ax.axis("off")
+    ax.set_xlim(-1.0, 10.0)
+    ax.set_ylim(-1.5, 5.5)
+    legend_handles = [
+        Line2D(
+            [0],
+            [0],
+            marker="o",
+            color="w",
+            markerfacecolor=CHOICE_COLOR[choice],
+            markeredgecolor="k",
+            markersize=12,
+            label=CHOICE_NAME[choice],
+        )
+        for choice in (1, 0, 2)
+    ]
+    # place the legend in the open interior of the U so it clears the legs
+    ax.legend(handles=legend_handles, loc="center", frameon=False)
+    if title is not None:
+        ax.set_title(title, fontsize=13)
+
+    fig.savefig(f"{out_path}.png", dpi=200, bbox_inches="tight")
+    fig.savefig(f"{out_path}.pdf", bbox_inches="tight")
+    plt.close(fig)
+
+
+def design_from_csv(csv_path: str) -> np.ndarray:
+    """Read x0..x10 from a best_bootstrap_solution CSV."""
+    row = pd.read_csv(csv_path).iloc[0]
+    return np.array([int(row[f"x{i}"]) for i in range(11)])
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Plot a design schematic")
+    parser.add_argument(
+        "-i", "--input", required=True, help="best_bootstrap_solution CSV"
+    )
+    parser.add_argument(
+        "-o", "--out", default="optimum_schematic", help="output path (no ext)"
+    )
+    parser.add_argument("-t", "--title", default=None)
+    args = parser.parse_args()
+
+    plot_schematic(design_from_csv(args.input), args.out, title=args.title)
+    print(f"Wrote {args.out}.png / .pdf")
diff --git a/papers/scaleup/SA_optimization/plot_marginal_gain.py b/papers/scaleup/SA_optimization/plot_marginal_gain.py
new file mode 100644
index 00000000..cdc4926e
--- /dev/null
+++ b/papers/scaleup/SA_optimization/plot_marginal_gain.py
@@ -0,0 +1,72 @@
+import os
+
+import pandas as pd
+from prettyPlot.plotting import plt, pretty_labels
+
+QOI_LABELS = {
+    "qoi": {
+        "label": "QOI",
+        # "ylabel": r"Optimal QOI [kg$^2$/kWh$^2$]",
+        "ylabel": r"Optimal QOI$_1$ [kg$^2$/kWh$^2$]",
+    },
+    "qoi_kla": {
+        "label": "QOI Num",
+        # "ylabel": r"Optimal QOI Num [kg$^2$/s$^2$]",
+        "ylabel": r"Optimal QOI$_2$ [kg$^2$/s$^2$]",
+    },
+    "qoi_sum": {
+        "label": "QOI Sum",
+        # "ylabel": r"Optimal QOI Sum [kg/kWh]",
+        "ylabel": r"Optimal QOI$_3$ [kg/kWh]",
+    },
+    "qoi_sum_kla": {
+        "label": "QOI Sum Num",
+        # "ylabel": r"Optimal QOI Sum Num [kg/s]",
+        "ylabel": r"Optimal QOI$_4$ [kg/s]",
+    },
+}
+
+LEVEL_TITLES = {
+    "lev1": "3.6 L reactor",
+    "lev6": r"608 m$^3$ reactor",
+}
+
+
+if __name__ == "__main__":
+    df = pd.read_csv("marginal_gain_results.csv")
+
+    for level in df["level"].unique():
+        df_lev = df[df["level"] == level]
+        for qoi_name in df_lev["qoi_name"].unique():
+            df_q = df_lev[df_lev["qoi_name"] == qoi_name].sort_values(
+                "n_spargers"
+            )
+            info = QOI_LABELS[qoi_name]
+
+            n_spargers = df_q["n_spargers"].values[:-1]
+            mean_optimum = df_q["optimal_qoi_mean"].values[:-1]
+            ci95 = df_q["optimal_qoi_ci95"].values[:-1]
+
+            fig, ax = plt.subplots()
+            ax.plot(n_spargers, mean_optimum, linewidth=3, color="k")
+            ax.fill_between(
+                n_spargers,
+                mean_optimum - ci95,
+                mean_optimum + ci95,
+                color="k",
+                alpha=0.25,
+                label="95% CI",
+            )
+            pretty_labels(
+                r"N$_{\rm sparg}$",
+                info["ylabel"],
+                20,
+                fontname="Times",
+                grid=False,
+                title=LEVEL_TITLES.get(level, level),
+            )
+            fname = f"marginal_gain_{level}_{qoi_name}"
+            plt.savefig(f"{fname}.png", dpi=300)
+            plt.savefig(f"{fname}.pdf")
+            plt.close()
+            print(f"Saved {fname}.png/.pdf")
diff --git a/papers/scaleup/SA_optimization/surrogate.py b/papers/scaleup/SA_optimization/surrogate.py
new file mode 100644
index 00000000..565ecac8
--- /dev/null
+++ b/papers/scaleup/SA_optimization/surrogate.py
@@ -0,0 +1,273 @@
+import warnings
+
+import numpy as np
+import optuna
+import torch
+import torch.nn as nn
+from scipy.interpolate import RBFInterpolator
+from sklearn.ensemble import RandomForestRegressor
+from sklearn.metrics import mean_squared_error
+from sklearn.preprocessing import OneHotEncoder, StandardScaler
+
+warnings.filterwarnings("ignore")
+optuna.logging.set_verbosity(optuna.logging.WARNING)
+
+# epsilon-using RBF kernels (so tuning epsilon stays meaningful for each)
+RBF_KERNELS = (
+    "multiquadric",
+    "inverse_multiquadric",
+    "inverse_quadratic",
+    "gaussian",
+)
+
+# the 11 design variables are unordered categoricals {0=mixer, 1=sparger, 2=wall}
+DESIGN_CATEGORIES = (0, 1, 2)
+
+
+def make_encoder(n_features: int = 11) -> OneHotEncoder:
+    """One-hot encoder shared by all surrogates.
+
+    Categories are fixed to {0, 1, 2} for every design variable so the encoded
+    width is always 3 x n_features, regardless of which values happen to appear
+    in a given train/bootstrap subset.
+    """
+    return OneHotEncoder(
+        categories=[list(DESIGN_CATEGORIES)] * n_features,
+        sparse_output=False,
+        handle_unknown="ignore",
+    )
+
+
+def check_data_shape(X: np.ndarray, y: np.ndarray) -> None:
+    """Validate shapes: (N, d) for X, (N, 1) for y."""
+    assert X.shape[0] == y.shape[0]
+    assert len(X.shape) == 2
+    assert len(y.shape) == 2
+    assert y.shape[1] == 1
+    print(f"INFO: {X.shape[0]} sim with {X.shape[1]} design variables")
+
+
+def tune_rbf(
+    X_train: np.ndarray,
+    y_train: np.ndarray,
+    X_test: np.ndarray,
+    y_test: np.ndarray,
+    n_trials: int = 100,
+) -> dict:
+    """Tune RBF epsilon + kernel type by MSE on a held-out test set."""
+    check_data_shape(X=X_train, y=y_train)
+    check_data_shape(X=X_test, y=y_test)
+    encoder = make_encoder(X_train.shape[1])
+    X_train_enc = encoder.fit_transform(X_train)
+    X_test_enc = encoder.transform(X_test)
+    y_scaler = StandardScaler().fit(y_train)
+    y_train_s = y_scaler.transform(y_train)
+    y_test_s = y_scaler.transform(y_test)
+
+    def objective(trial):
+        kernel = trial.suggest_categorical("kernel", list(RBF_KERNELS))
+        epsilon = trial.suggest_float("epsilon", 0.1, 10.0, log=False)
+        try:
+            model = RBFInterpolator(
+                X_train_enc, y_train_s, epsilon=epsilon, kernel=kernel
+            )
+            return mean_squared_error(y_test_s, model(X_test_enc))
+        except Exception:
+            return float("inf")
+
+    study = optuna.create_study(direction="minimize")
+    study.optimize(objective, n_trials=n_trials)
+    return study.best_params
+
+
+def tune_rf(
+    X_train: np.ndarray,
+    y_train: np.ndarray,
+    X_test: np.ndarray,
+    y_test: np.ndarray,
+    n_trials: int = 100,
+) -> dict:
+    """Tune RandomForest hyperparameters by MSE on a held-out test set."""
+    check_data_shape(X=X_train, y=y_train)
+    check_data_shape(X=X_test, y=y_test)
+    encoder = make_encoder(X_train.shape[1])
+    X_train_enc = encoder.fit_transform(X_train)
+    X_test_enc = encoder.transform(X_test)
+    y_scaler = StandardScaler().fit(y_train)
+    y_train_s = y_scaler.transform(y_train)
+    y_test_s = y_scaler.transform(y_test)
+
+    def objective(trial):
+        model = RandomForestRegressor(
+            n_estimators=trial.suggest_int("n_estimators", 50, 200),
+            max_depth=trial.suggest_int("max_depth", 3, 10),
+            min_samples_leaf=trial.suggest_int("min_samples_leaf", 1, 10),
+            max_features=trial.suggest_float("max_features", 0.1, 1.0),
+            random_state=42,
+        )
+        model.fit(X_train_enc, y_train_s.ravel())
+        return mean_squared_error(y_test_s, model.predict(X_test_enc))
+
+    study = optuna.create_study(direction="minimize")
+    study.optimize(objective, n_trials=n_trials)
+    return study.best_params
+
+
+def tune_nn(
+    X_train: np.ndarray,
+    y_train: np.ndarray,
+    X_test: np.ndarray,
+    y_test: np.ndarray,
+    n_trials: int = 100,
+) -> dict:
+    """Tune NN units, layers, and learning rate by MSE on a held-out test set."""
+    check_data_shape(X=X_train, y=y_train)
+    check_data_shape(X=X_test, y=y_test)
+    encoder = make_encoder(X_train.shape[1])
+    X_train_enc = encoder.fit_transform(X_train)
+    X_test_enc = encoder.transform(X_test)
+    y_scaler = StandardScaler().fit(y_train)
+    y_train_s = y_scaler.transform(y_train)
+    y_test_s = y_scaler.transform(y_test)
+
+    def objective(trial):
+        units = trial.suggest_int("n_units", 16, 128)
+        layers = trial.suggest_int("n_layers", 1, 3)
+        lr = trial.suggest_float("lr", 1e-4, 1e-2, log=True)
+        model = _build_nn(X_train_enc.shape[1], units, layers)
+        _train_nn(model, X_train_enc, y_train_s, lr=lr)
+        with torch.no_grad():
+            X_t = torch.tensor(X_test_enc, dtype=torch.float32)
+            preds = model(X_t).numpy().flatten()
+        return mean_squared_error(y_test_s, preds)
+
+    study = optuna.create_study(direction="minimize")
+    study.optimize(objective, n_trials=n_trials)
+    return study.best_params
+
+
+def _build_nn(input_dim: int, units: int, layers: int) -> nn.Sequential:
+    """Build a PyTorch Sequential model."""
+    layer_list = [nn.Linear(input_dim, units), nn.ReLU()]
+    for _ in range(layers - 1):
+        layer_list.extend([nn.Linear(units, units), nn.ReLU()])
+    layer_list.append(nn.Linear(units, 1))
+    return nn.Sequential(*layer_list)
+
+
+def _train_nn(
+    model: nn.Sequential,
+    X: np.ndarray,
+    y: np.ndarray,
+    epochs: int = 1000,
+    lr: float = 1e-3,
+    patience: int = 50,
+    val_frac: float = 0.15,
+    min_delta: float = 1e-5,
+) -> None:
+    """Train in-place (full-batch Adam) with early stopping.
+
+    A fraction ``val_frac`` of the passed data is held out to monitor validation
+    loss; training stops once it has not improved by ``min_delta`` for
+    ``patience`` consecutive epochs, and the best weights are restored. The
+    holdout is carved from the training data given here, so it never touches the
+    outer test/validation split.
+    """
+    n_samples = X.shape[0]
+    n_val = int(round(n_samples * val_frac))
+    perm = np.random.default_rng(0).permutation(n_samples)
+    val_idx, train_idx = perm[:n_val], perm[n_val:]
+    if n_val < 1 or train_idx.size < 1:  # too small to hold out: monitor train
+        val_idx = train_idx = np.arange(n_samples)
+
+    X_train = torch.tensor(X[train_idx], dtype=torch.float32)
+    y_train = torch.tensor(y[train_idx], dtype=torch.float32)
+    X_val = torch.tensor(X[val_idx], dtype=torch.float32)
+    y_val = torch.tensor(y[val_idx], dtype=torch.float32)
+
+    optimizer = torch.optim.Adam(model.parameters(), lr=lr)
+    loss_fn = nn.MSELoss()
+    best_val_loss = float("inf")
+    best_state = None
+    epochs_without_improvement = 0
+    for _ in range(epochs):
+        model.train()
+        optimizer.zero_grad()
+        loss_fn(model(X_train), y_train).backward()
+        optimizer.step()
+        model.eval()
+        with torch.no_grad():
+            val_loss = float(loss_fn(model(X_val), y_val))
+        if val_loss < best_val_loss - min_delta:
+            best_val_loss = val_loss
+            best_state = {
+                name: t.detach().clone()
+                for name, t in model.state_dict().items()
+            }
+            epochs_without_improvement = 0
+        else:
+            epochs_without_improvement += 1
+            if epochs_without_improvement >= patience:
+                break
+    if best_state is not None:
+        model.load_state_dict(best_state)
+    model.eval()
+
+
+class Surrogate_wrapper:
+    """Unified predict() interface for RBF, RF, and NN surrogates.
+
+    All three share one one-hot encoding of the raw {0, 1, 2} design variables
+    and one standardization of the targets, both fit here on the training data.
+    Targets are standardized before fitting; predict() inverse-transforms so its
+    return value is always in physical units. predict() takes a raw design vector
+    and encodes it, so the caller (simulated annealing) stays in raw design space.
+    """
+
+    def __init__(
+        self,
+        model_type: str,
+        X: np.ndarray,
+        y: np.ndarray,
+        params: dict,
+    ):
+        self.model_type = model_type.lower()
+        self.encoder = make_encoder(X.shape[1])
+        X_encoded = self.encoder.fit_transform(X)
+        self.y_scaler = StandardScaler().fit(y)
+        y_scaled = self.y_scaler.transform(y)
+
+        if self.model_type == "rbf":
+            self.model = RBFInterpolator(
+                X_encoded,
+                y_scaled,
+                kernel=params.get("kernel", "multiquadric"),
+                epsilon=params["epsilon"],
+            )
+        elif self.model_type == "rf":
+            self.model = RandomForestRegressor(**params, random_state=42)
+            self.model.fit(X_encoded, y_scaled.ravel())
+        elif self.model_type == "nn":
+            self.model = _build_nn(
+                X_encoded.shape[1],
+                params["n_units"],
+                params["n_layers"],
+            )
+            _train_nn(
+                self.model, X_encoded, y_scaled, lr=params.get("lr", 1e-3)
+            )
+        else:
+            raise NotImplementedError(f"Unknown model_type: {model_type}")
+
+    def predict(self, X: np.ndarray) -> float:
+        """Return the physical-space prediction for one raw design vector."""
+        X_enc = self.encoder.transform(X.reshape(1, -1))
+        if self.model_type == "nn":
+            with torch.no_grad():
+                X_t = torch.tensor(X_enc, dtype=torch.float32)
+                scaled = self.model(X_t).item()
+        elif self.model_type == "rf":
+            scaled = self.model.predict(X_enc)[0]
+        else:
+            scaled = float(np.squeeze(self.model(X_enc)))
+        return float(self.y_scaler.inverse_transform([[scaled]])[0, 0])
diff --git a/papers/scaleup/SA_optimization/surrogate_selection.csv b/papers/scaleup/SA_optimization/surrogate_selection.csv
new file mode 100644
index 00000000..23773d57
--- /dev/null
+++ b/papers/scaleup/SA_optimization/surrogate_selection.csv
@@ -0,0 +1,9 @@
+level,qoi_name,best,val_mse,val_nrmse_amp_pct,val_nrmse_mean_pct,best_params
+lev6,qoi,nn,2.5414217695066155,10.346422847895706,12.51112854539323,"{'n_units': 23, 'n_layers': 2, 'lr': 0.0009480593464653759}"
+lev6,qoi_kla,nn,0.0006345451226036295,10.660299052886097,12.626611466642379,"{'n_units': 36, 'n_layers': 2, 'lr': 0.009975314935443623}"
+lev6,qoi_sum,nn,3.1047786209819535,8.802302307279254,5.488729982414982,"{'n_units': 38, 'n_layers': 2, 'lr': 0.009796559328428031}"
+lev6,qoi_sum_kla,rbf,0.0639246836136791,10.31320641871671,6.2904200932450625,"{'kernel': 'multiquadric', 'epsilon': 0.2921716473956134}"
+lev1,qoi,nn,0.04559337741600136,0.6704719275922347,18.426961145633662,"{'n_units': 115, 'n_layers': 3, 'lr': 0.007352422228350128}"
+lev1,qoi_kla,nn,1.4334769254169032e-26,4.152094975112983,29.08632682734781,"{'n_units': 58, 'n_layers': 3, 'lr': 0.004000778796522329}"
+lev1,qoi_sum,nn,0.6018713490278378,3.2021518530766255,10.45378113072208,"{'n_units': 32, 'n_layers': 3, 'lr': 0.003626140666750365}"
+lev1,qoi_sum_kla,nn,3.7395053463098084e-13,12.835729422646637,9.480054040832073,"{'n_units': 52, 'n_layers': 2, 'lr': 0.00027717283587404306}"
diff --git a/papers/scaleup/generate_scaleup_runs/README.md b/papers/scaleup/generate_scaleup_runs/README.md
new file mode 100644
index 00000000..9bca124a
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/README.md
@@ -0,0 +1,3 @@
+`python randsim.py` generates study folders that contain an ensemble of Openfoam case folders, each with a different design variable sample
+
+The case folders use `template` as a template openfoam folder to create the new openfoam case folders. 
diff --git a/papers/scaleup/generate_scaleup_runs/randsim.py b/papers/scaleup/generate_scaleup_runs/randsim.py
new file mode 100644
index 00000000..6b518e3d
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/randsim.py
@@ -0,0 +1,163 @@
+import os
+
+import numpy as np
+
+from bird.preprocess.json_gen.design_io import *
+from bird.preprocess.json_gen.generate_designs import *
+
+
+def optimization_setup():
+    # spots on the branches where we can place sparger or mixers
+    branchcom_spots = {}
+    branchcom_spots[0] = np.linspace(0.2, 0.8, 4)
+    branchcom_spots[1] = np.linspace(0.2, 0.8, 3)
+    branchcom_spots[2] = np.linspace(0.2, 0.8, 4)
+    # branches where the sparger and mixers are placed
+    branches_com = [0, 1, 2]
+    return branchcom_spots, branches_com
+
+
+# Shared design pool
+# once it is generated, all the other studies borrow this file
+# This is useful to check if QOI values match and are correlated
+DESIGN_FILE = os.path.join(
+    os.path.dirname(os.path.abspath(__file__)), "designs.pkl"
+)
+
+
+if __name__ == "__main__":
+    branchcom_spots, branches_com = optimization_setup()
+
+    config_dict = load_or_sample_designs(
+        DESIGN_FILE, branches_com, branchcom_spots, n_designs=400
+    )
+
+    # --- hyperparameters of the study
+    vvm = 0.4
+    constantD = True
+    # Dynamic mixer properties
+    # The sign business is because orientation depends on the branch
+    # so that the mixer pushes the flow consistently
+    mixer_params = {
+        "Np": 6,
+        "Vtip": 1.5,
+        "sigma": 0.35,
+        "radius": 0.4,
+        "sign": {0: "+", 1: "+", 2: "-"},
+        "swirl_sign": {0: "+", 1: "+", 2: "-"},
+    }
+
+    # --- Setup the scale up study
+    # lev1 = 3.6 L, lev6 = 608 m3
+    # 400 runs for lev 1 and lev 6
+    # 200 runs for intermediate scales (match first 200 design variables
+    # of the 400 pool)
+    levels = [
+        ("lev1", 0.05, 400),
+        ("lev2", 0.1, 200),
+        ("lev3", 0.2, 200),
+        ("lev4", 0.4, 200),
+        ("lev5", 0.8, 200),
+        ("lev6", 2.7615275385627096, 400),
+    ]
+
+    # Per-level system/controlDict time-stepping.
+    # Coarser scales (higher levels) tolerate initial dt
+    level_controldict = {
+        "lev1": {
+            "maxCo": "0.25",
+            "maxDeltaT": "0.00025",
+            "deltaT": "1e-5",
+            "endTime": "100",
+        },
+        "lev2": {
+            "maxCo": "0.25",
+            "maxDeltaT": "0.0005",
+            "deltaT": "2e-5",
+            "endTime": "200",
+        },
+        "lev3": {
+            "maxCo": "0.25",
+            "maxDeltaT": "0.001",
+            "deltaT": "4e-5",
+            "endTime": "400",
+        },
+        "lev4": {
+            "maxCo": "0.25",
+            "maxDeltaT": "0.002",
+            "deltaT": "5e-5",
+            "endTime": "400",
+        },
+        "lev5": {
+            "maxCo": "0.25",
+            "maxDeltaT": "0.004",
+            "deltaT": "5e-5",
+            "endTime": "400",
+        },
+        "lev6": {
+            "maxCo": "0.25",
+            "maxDeltaT": "0.005",
+            "deltaT": "1e-4",
+            "endTime": "400",
+        },
+    }
+
+    # Per-level get_qoi.py parameters
+    # gas density [kg/m3] at spargers change because of varying reactor height
+    # c* (low, high) uniform-prior bounds on the CO2/H2 depend on scale
+    level_qoi = {
+        "lev1": {
+            "rhog": 0.593333,
+            "cstar_co2": (7.68, 8.22),
+            "cstar_h2": (0.516, 0.548),
+        },
+        "lev2": {
+            "rhog": 0.605962,
+            "cstar_co2": (6.8, 7.93),
+            "cstar_h2": (0.502, 0.514),
+        },
+        "lev3": {
+            "rhog": 0.629974,
+            "cstar_co2": (7.04, 8.06),
+            "cstar_h2": (0.537, 0.557),
+        },
+        "lev4": {
+            "rhog": 0.677935,
+            "cstar_co2": (8.3, 9.8),
+            "cstar_h2": (0.564, 0.601),
+        },
+        "lev5": {
+            "rhog": 0.770533,
+            "cstar_co2": (7.89, 10.2),
+            "cstar_h2": (0.622, 0.653),
+        },
+        "lev6": {
+            "rhog": 1.25,
+            "cstar_co2": (14, 16.9),
+            "cstar_h2": (1.04, 1.19),
+        },
+    }
+
+    parent = "study"
+    for name, scale, n_sim in levels:
+        study_folder = os.path.join(parent, f"study_0_4vvm_{name}")
+        generate_leveled_reactor_cases(
+            config_dict,
+            branchcom_spots,
+            scale=scale,
+            n_sim=n_sim,
+            study_folder=study_folder,
+            mixer_params=mixer_params,
+            vvm=vvm,
+            template_folder="./template",
+            constantD=constantD,  # needs to be False if we do PBE
+            start_time=1,
+            account="gas2fuels",
+            cores_per_sim=8,  # Pack as many sims per node as possible
+            cores_per_node=104,
+            walltime="120:00:00",
+            controldict_params=level_controldict[name],
+            rhog=level_qoi[name]["rhog"],
+            cstar_co2=level_qoi[name]["cstar_co2"],
+            cstar_h2=level_qoi[name]["cstar_h2"],
+        )
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.gas
new file mode 100644
index 00000000..e4165b1a
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.gas
@@ -0,0 +1,47 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      CO2.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+dimensions      [0 0 0 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform 0;
+
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $f_CO2;
+    }
+
+    outlet
+    {
+        //type            inletOutlet;
+        //phi             phi.gas;
+        //inletValue      $f_CO2;
+        //value           $f_CO2;
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.liquid
new file mode 100644
index 00000000..4b8ea6a0
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.liquid
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      CO2.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 0.0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            zeroGradient;
+        //type            fixedValue;
+        //value           uniform 0.0;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/H2.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/H2.gas
new file mode 100644
index 00000000..9f66b2d2
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/H2.gas
@@ -0,0 +1,47 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      H2.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+dimensions      [0 0 0 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform 0;
+
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $f_H2;
+    }
+
+    outlet
+    {
+        //type            inletOutlet;
+        //phi             phi.gas;
+        //inletValue      $f_H2;
+        //value           $f_H2;
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/H2.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/H2.liquid
new file mode 100644
index 00000000..65ae8d34
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/H2.liquid
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      H2.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 0.0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            zeroGradient;
+        //type            fixedValue;
+        //value           uniform 0.0;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/N2.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/N2.gas
new file mode 100644
index 00000000..c1d7225f
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/N2.gas
@@ -0,0 +1,47 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      N2.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+dimensions      [0 0 0 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform 1;
+
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $f_N2;
+    }
+
+    outlet
+    {
+        //type            inletOutlet;
+        //phi             phi.gas;
+        //inletValue      $f_N2;
+        //value           $f_N2;
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/T.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/T.gas
new file mode 100644
index 00000000..bf0199a0
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/T.gas
@@ -0,0 +1,44 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      T.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 1 0 0 0];
+
+internalField   uniform 300;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           $internalField;
+    }
+
+    outlet
+    {
+        type            inletOutlet;
+        phi             phi.gas;
+        inletValue      $internalField;
+        value           $internalField;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/T.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/T.liquid
new file mode 100644
index 00000000..7101ea31
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/T.liquid
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      T.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 1 0 0 0];
+
+internalField   uniform 300;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    outlet
+    {
+        type            inletOutlet;
+        phi             phi.liquid;
+        inletValue      $internalField;
+        value           $internalField;
+    }
+    inlet
+    {
+        type            fixedValue;
+        value           $internalField;
+    }
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/U.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/U.gas
new file mode 100644
index 00000000..e696566f
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/U.gas
@@ -0,0 +1,47 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volVectorField;
+    object      U.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -1 0 0 0 0];
+
+internalField   uniform (0 0.0 0);
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        //type            flowRateInletVelocity;
+        //massFlowRate    $mflowRateGas;
+        //rho             thermo:rho.gas;
+        //value           $internalField;
+        type            fixedValue;
+        value           uniform (0 $uGasPhase 0);       
+    }
+    outlet
+    {
+        type            pressureInletOutletVelocity;
+        phi             phi.gas;
+        value           $internalField;
+    }
+    defaultFaces
+    {
+        type            slip;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/U.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/U.liquid
new file mode 100644
index 00000000..1879e020
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/U.liquid
@@ -0,0 +1,46 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volVectorField;
+    object      U.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -1 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform (0 0 0);
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"  
+
+    inlet
+    {
+        //type            flowRateInletVelocity;
+        //massFlowRate    $mflowRateLiq;
+        //rho             thermo:rho.liquid;
+        //value           $internalField;
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    outlet
+    {
+        type            noSlip;
+    }
+    defaultFaces
+    {
+        type            noSlip;
+    }
+
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.gas
new file mode 100644
index 00000000..fba2945d
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.gas
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      Ydefault.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 0.0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 0.0;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.liquid
new file mode 100644
index 00000000..a5108564
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.liquid
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      Ydefault.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 1.0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 1.0;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.gas
new file mode 100644
index 00000000..1e303fbe
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.gas
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      alpha.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform $alphaGas;
+
+boundaryField
+{
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $alphaGas;
+    }
+    outlet
+    {
+        type            inletOutlet;
+        phi             phi.gas;
+        inletValue      uniform 1;
+        value           uniform 1;
+    }
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.liquid
new file mode 100644
index 00000000..5c92070b
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.liquid
@@ -0,0 +1,40 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      alpha.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform 1;
+
+boundaryField
+{
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $alphaLiq;
+    }
+    outlet
+    {
+        type            fixedValue;
+        value           uniform 0;
+    }
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.gas
new file mode 100644
index 00000000..b867958f
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.gas
@@ -0,0 +1,46 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      alphat.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -1 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    outlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    defaultFaces
+    {
+        type            calculated;
+        value           $internalField;
+        //type            compressible::alphatWallFunction;
+        //Prt             0.85;
+        //value           $internalField;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.liquid
new file mode 100644
index 00000000..2569c3ee
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.liquid
@@ -0,0 +1,44 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      alphat.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -1 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    outlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    defaultFaces
+    {
+        type            compressible::alphatWallFunction;
+        Prt             0.85;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/f.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/f.gas
new file mode 100644
index 00000000..76ee77a9
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/f.gas
@@ -0,0 +1,41 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      f.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 1.0;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 1.0; //$internalField; //
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/k.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/k.gas
new file mode 100644
index 00000000..4a3d44ca
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/k.gas
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      k.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -2 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform $k_inlet_gas;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type           fixedValue;
+        value          uniform $k_inlet_gas;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/k.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/k.liquid
new file mode 100644
index 00000000..cde8f6c1
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/k.liquid
@@ -0,0 +1,44 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      k.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -2 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform $k_inlet_liq;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type           fixedValue;
+        value          uniform $k_inlet_liq;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            kqRWallFunction;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/nut.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/nut.gas
new file mode 100644
index 00000000..ba16dd4c
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/nut.gas
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      nut.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -1 0 0 0 0];
+
+internalField   uniform 1e-8;
+
+boundaryField
+{
+    inlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    outlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    defaultFaces
+    {
+        //type            nutkWallFunction;
+        //value           $internalField;
+        type            calculated;
+        value           $internalField;
+    }
+
+    // defaultFaces
+    // {
+    //     type            empty;
+    // }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/nut.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/nut.liquid
new file mode 100644
index 00000000..1442e07f
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/nut.liquid
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      nut.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -1 0 0 0 0];
+
+internalField   uniform 1e-4;
+
+boundaryField
+{
+    #includeEtc "caseDicts/setConstraintTypes"
+
+    inlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    outlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+
+    defaultFaces
+    {
+        type            nutkWallFunction;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/omega.gas b/papers/scaleup/generate_scaleup_runs/template/0.orig/omega.gas
new file mode 100644
index 00000000..9a1b4816
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/omega.gas
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      omega.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 -1 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform $omega_inlet_gas;
+
+boundaryField
+{
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $omega_inlet_gas;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            zeroGradient;
+        //type            epsilonWallFunction;
+        //value         $internalField;
+    }
+
+    // defaultFaces
+    // {
+    //     type            empty;
+    // }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/omega.liquid b/papers/scaleup/generate_scaleup_runs/template/0.orig/omega.liquid
new file mode 100644
index 00000000..821a806d
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/omega.liquid
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      omega.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 -1 0 0 0 0];
+
+#include "${FOAM_CASE}/constant/globalVars"
+
+internalField   uniform $omega_inlet_liq;
+
+boundaryField
+{
+    inlet
+    {
+        type            fixedValue;
+        value           uniform $omega_inlet_liq;
+    }
+
+    outlet
+    {
+        type            zeroGradient;
+    }
+
+    defaultFaces
+    {
+        type            omegaWallFunction;
+        value           $internalField;
+    }
+
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/p b/papers/scaleup/generate_scaleup_runs/template/0.orig/p
new file mode 100644
index 00000000..b3a295fb
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/p
@@ -0,0 +1,39 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions          [1 -1 -2 0 0 0 0];
+
+internalField       uniform 101325;
+
+boundaryField
+{
+    inlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+    outlet
+    {
+        type            calculated;
+        value           $internalField;
+    }
+    defaultFaces
+    {
+        type            calculated;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/0.orig/p_rgh b/papers/scaleup/generate_scaleup_runs/template/0.orig/p_rgh
new file mode 100644
index 00000000..88ee7d80
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/0.orig/p_rgh
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       volScalarField;
+    object      p_rgh;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions          [1 -1 -2 0 0 0 0];
+
+internalField       uniform 101325;
+
+boundaryField
+{
+    inlet
+    {
+        type            fixedFluxPressure;
+        value           $internalField;
+    }
+    outlet
+    {
+        type            prghTotalPressure;
+        p0              $internalField;
+        U               U.gas;
+        phi             phi.gas;
+        rho             thermo:rho.gas;
+        value           $internalField;
+    }
+    defaultFaces
+    {
+        type            fixedFluxPressure;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/Allclean b/papers/scaleup/generate_scaleup_runs/template/Allclean
new file mode 100755
index 00000000..f55e0ec9
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/Allclean
@@ -0,0 +1,18 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+# Remove surface, features and solution
+#rm -rf constant/extendedFeatureEdgeMesh > /dev/null 2>&1
+#rm -f constant/triSurface/*.eMesh > /dev/null 2>&1
+#rm -rf constant/polyMesh > /dev/null 2>&1
+#rm -rf processor* > /dev/null 2>&1
+rm -rf 0
+cleanCase
+
+#rm *.obj
+#rm *.stl
+
+#------------------------------------------------------------------------------
diff --git a/papers/scaleup/generate_scaleup_runs/template/computeQOI.sh b/papers/scaleup/generate_scaleup_runs/template/computeQOI.sh
new file mode 100644
index 00000000..800e45d4
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/computeQOI.sh
@@ -0,0 +1,13 @@
+if [ ! -f qoi.txt ]; then
+    # Reconstruct if needed
+    source /projects/gas2fuels/ofoam_cray_mpich/OpenFOAM-dev/etc/bashrc
+    reconstructPar -newTimes
+    module load conda
+    conda activate /projects/gas2fuels/conda_env/bird_mixer/
+    python read_history.py -cr .. -cn local -df data
+    python get_qoi.py
+    conda deactivate
+else
+   echo "WARNING: QOI already computed"
+fi
+
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/fvModels b/papers/scaleup/generate_scaleup_runs/template/constant/fvModels
new file mode 100644
index 00000000..353551df
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/fvModels
@@ -0,0 +1,128 @@
+FoamFile
+{
+	version  9.0;
+	format   ascii;
+	class    dictionary;
+	location "constant";
+	object   fvModels;
+}
+
+codedSource
+{
+	type	coded;
+	selectionMode	all;
+	field	U.liquid;
+	name	sourceTime;
+
+	codeInclude
+	#{
+		#include "dynamicMix_util.H"
+	#};
+
+	codeOptions
+	#{
+		-I${FOAM_CASE}/constant
+	#};
+	codeAddAlphaRhoSup
+	#{
+		const Time& time = mesh().time();
+		const scalarField& V = mesh().V();
+		vectorField& Usource = eqn.source();
+		const vectorField& C = mesh().C();
+		const volScalarField& rhoL =
+			mesh().lookupObject<volScalarField>("thermo:rho.liquid");
+		const volScalarField& alphaL =
+			mesh().lookupObject<volScalarField>("alpha.liquid");
+		const volVectorField& UL =
+			mesh().lookupObject<volVectorField>("U.liquid");
+		double pi=3.141592654;
+		double source_pt_x=13.807637692813548;
+		double source_pt_y=1.3807637692813548;
+		double source_pt_z=12.426873923532193;
+		double disk_rad=0.9665346384969483;
+		double disk_area=pi*disk_rad*disk_rad;
+		double power=7626.034346240216;
+		double smear_factor=3.0;
+		const scalar startTime = 1;
+		if (time.value() > startTime)
+		{
+			// Get V1
+			double source_sign_factor = 1.0;
+			double V1 = 0;
+			double V2 = 0;
+			double rhoV;
+			double dist_tol = disk_rad*5;
+
+			double dist_n;
+			double upV = 0;
+			double uprhoV = 0;
+			double upVvol = 0;
+			double downV = 0;
+			double downrhoV = 0;
+			double downVvol = 0;
+			double dist2;
+			forAll(C,i)
+			{
+				dist2 = (C[i].x()-source_pt_x)*(C[i].x()-source_pt_x);
+				dist2 += (C[i].y()-source_pt_y)*(C[i].y()-source_pt_y);
+				dist2 += (C[i].z()-source_pt_z)*(C[i].z()-source_pt_z);
+
+				dist_n = (C[i].x()-source_pt_x);
+
+				if (dist2 < dist_tol*dist_tol && dist_n < -dist_tol/2) {
+					upVvol += V[i] * alphaL[i];
+					upV += V[i] * alphaL[i] * UL[i][0];
+					uprhoV += V[i] * alphaL[i] * rhoL[i];
+				}
+				if (dist2 < dist_tol*dist_tol && dist_n > dist_tol/2) {
+					downVvol += V[i] * alphaL[i];
+					downV += V[i] * alphaL[i] * UL[i][0];
+					downrhoV += V[i] * alphaL[i] * rhoL[i];
+				}
+			}
+
+			reduce(uprhoV, sumOp<scalar>());
+			reduce(downrhoV, sumOp<scalar>());
+			reduce(upV, sumOp<scalar>());
+			reduce(downV, sumOp<scalar>());
+			reduce(downVvol, sumOp<scalar>());
+			reduce(upVvol, sumOp<scalar>());
+
+			downV /= downVvol;
+			upV /= upVvol;
+			downrhoV /= downVvol;
+			uprhoV /= upVvol;
+
+			if (upV <= 0 && downV <= 0) {
+				source_sign_factor = -1.0;
+				V1 = std::abs(upV);
+				rhoV = uprhoV;
+			} else if (upV >= 0 && downV >= 0) {
+				source_sign_factor = 1.0;
+				V1 = std::abs(downV);
+				rhoV = downrhoV;
+			} else {
+				V1 = 0.0;
+				source_sign_factor = -1.0;
+				rhoV = uprhoV;
+				Foam::Info << "[BIRD:DYNMIX WARN] " << "upV = " << upV << " downV = " << downV << " for source at " << source_pt_x << ", " << source_pt_y << ", " << source_pt_z <<  endl;
+			}
+			Foam::Info << "[BIRD:DYNMIX INFO] V1 = " << V1 << endl;
+			
+			// Get V2
+			V2 = findV2(power, rhoV, disk_area, V1);
+
+			forAll(C,i)
+			{
+				double Thrust=0.5*rhoL[i]*(V2*V2 - V1*V1)*disk_area;
+				double dist2=(C[i].x()-source_pt_x)*(C[i].x()-source_pt_x);
+				dist2 += (C[i].y()-source_pt_y)*(C[i].y()-source_pt_y);
+				dist2 += (C[i].z()-source_pt_z)*(C[i].z()-source_pt_z);
+				double epsilon=pow(V[i],0.33333)*smear_factor;
+				double sourceterm=alphaL[i]*(Thrust/pow(pi,1.5)/pow(epsilon,3.0))*
+					exp(-dist2/(epsilon*epsilon));
+				Usource[i][0] -=  source_sign_factor*sourceterm*V[i];
+			}
+		}
+	#};
+};
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/g b/papers/scaleup/generate_scaleup_runs/template/constant/g
new file mode 100644
index 00000000..770a5619
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/g
@@ -0,0 +1,21 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       uniformDimensionedVectorField;
+    location    "constant";
+    object      g;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -2 0 0 0 0];
+value           (0 -9.81 0);
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/globalVars b/papers/scaleup/generate_scaleup_runs/template/constant/globalVars
new file mode 100644
index 00000000..1a0ce724
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/globalVars
@@ -0,0 +1,83 @@
+T0	300; //initial T(K) which stays constant
+VVM	1.6;
+//****water Liquid properties**************
+CpMixLiq        4181;
+muMixLiq #calc "2.414e-5 * pow(10,247.8/($T0 - 140.0))"; //viscosity (Pa.s) of water as a function of T(K)  
+kThermLiq       0.62; // W/m-K
+rho0MixLiq      1000; // kg/m^3
+sigmaLiq        0.07; //surface tension N/m
+//Wilke-Chang params for diffusion coefficient of a given solute in water (solvent)
+WC_psi          2.6;
+WC_M            18; // kg/kmol
+WC_V_O2         25.6e-3; // m3/kmol molar volume at normal boiling temperature (Treybal 1968) 
+WC_V_H2         14.3e-3; 
+WC_V_CO2        34e-3;
+WC_V_CO         30.7e-3;
+WC_V_N2		31.2e-3;
+WC_V_CH4        35e-3; // V_b[cm3/mol]=0.285*V_critical^1.048 (Tyn and Calus; ESTIMATING LIQUID MOLAL VOLUME; Processing, Volume 21, Issue 4, Pages 16 - 17)
+//****** diffusion coeff ***********
+D_H2 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_H2,0.6)"; 
+D_CO2 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_CO2,0.6)"; 
+D_CO #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_CO,0.6)";
+D_CH4 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_CH4,0.6)";
+D_N2 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_N2,0.6)";
+//****** Henry coeff ***************
+H_O2_298 0.032;
+DH_O2   1700;
+H_CO2_298 0.83;
+DH_CO2  2400;
+H_CO_298 0.023;
+DH_CO  1300;
+H_H2_298 0.019;
+DH_H2   500;
+H_CH4_298 0.032;
+DH_CH4   1900;
+H_N2_298 0.015;
+DH_N2   1300;
+He_H2  #calc "$H_H2_298 * exp($DH_H2 *(1. / $T0 - 1./298.15))";
+He_CO  #calc "$H_CO_298 * exp($DH_CO *(1. / $T0 - 1./298.15))";
+He_CO2 #calc "$H_CO2_298 * exp($DH_CO2 *(1. / $T0 - 1./298.15))";
+He_CH4 #calc "$H_CH4_298 * exp($DH_CH4 *(1. / $T0 - 1./298.15))";
+He_N2 #calc "$H_N2_298 * exp($DH_N2 *(1. / $T0 - 1./298.15))";
+//*******inlet gas frac*************
+f_H2 0.1;
+f_CO2 0.9;
+f_N2 0.0;
+//*******inlet gas frac*************
+inletA	11.8966;
+liqVol	606.514;
+alphaGas 1;
+alphaLiq 0;
+uGasPhase #calc "$liqVol * $VVM / (60 * $inletA * $alphaGas)";
+//*********************************
+LeLiqH2 #calc "$kThermLiq / $rho0MixLiq / $D_H2 / $CpMixLiq";
+LeLiqCO #calc "$kThermLiq / $rho0MixLiq / $D_CO / $CpMixLiq";
+LeLiqCO2 #calc "$kThermLiq / $rho0MixLiq / $D_CO2 / $CpMixLiq"; // = 74
+LeLiqCH4 #calc "$kThermLiq / $rho0MixLiq / $D_CH4 / $CpMixLiq";
+LeLiqN2 #calc "$kThermLiq / $rho0MixLiq / $D_N2 / $CpMixLiq";
+LeLiqMix #calc "$f_CO2*$LeLiqCO2+$f_H2*$LeLiqH2";
+PrMixLiq #calc "$CpMixLiq * $muMixLiq / $kThermLiq";
+//*********************************
+kH2 #calc "$D_H2*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrH2 #calc "$muMixLiq*$CpMixLiq / $kH2";
+
+kCO #calc "$D_CO*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrCO #calc "$muMixLiq*$CpMixLiq / $kCO";
+
+kCO2 #calc "$D_CO2*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrCO2 #calc "$muMixLiq*$CpMixLiq / $kCO2";
+
+kCH4 #calc "$D_CH4*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrCH4 #calc "$muMixLiq*$CpMixLiq / $kCH4";
+
+kN2 #calc "$D_N2*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrN2 #calc "$muMixLiq*$CpMixLiq / $kN2";
+//*********************************
+l_scale 0.5;
+intensity 0.05;
+k_inlet_gas #calc "1.5 * Foam::pow(($uGasPhase), 2) * Foam::pow($intensity, 2)";
+k_inlet_liq #calc "1.5 * Foam::pow(($uGasPhase), 2) * Foam::pow($intensity, 2)";
+eps_inlet_gas #calc "pow(0.09,0.75) * Foam::pow($k_inlet_gas, 1.5) / ($l_scale * 0.07)";
+eps_inlet_liq #calc "pow(0.09,0.75) * Foam::pow($k_inlet_liq, 1.5) / ($l_scale * 0.07)";
+omega_inlet_gas #calc "pow(0.09,-0.25) * pow($k_inlet_gas,0.5) / ($l_scale * 0.07)";
+omega_inlet_liq #calc "pow(0.09,-0.25) * pow($k_inlet_liq,0.5) / ($l_scale * 0.07)";
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/globalVars_temp b/papers/scaleup/generate_scaleup_runs/template/constant/globalVars_temp
new file mode 100644
index 00000000..fcb076a7
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/globalVars_temp
@@ -0,0 +1,83 @@
+T0	300; //initial T(K) which stays constant
+VVM	0.2;
+//****water Liquid properties**************
+CpMixLiq        4181;
+muMixLiq #calc "2.414e-5 * pow(10,247.8/($T0 - 140.0))"; //viscosity (Pa.s) of water as a function of T(K)  
+kThermLiq       0.62; // W/m-K
+rho0MixLiq      1000; // kg/m^3
+sigmaLiq        0.07; //surface tension N/m
+//Wilke-Chang params for diffusion coefficient of a given solute in water (solvent)
+WC_psi          2.6;
+WC_M            18; // kg/kmol
+WC_V_O2         25.6e-3; // m3/kmol molar volume at normal boiling temperature (Treybal 1968) 
+WC_V_H2         14.3e-3; 
+WC_V_CO2        34e-3;
+WC_V_CO         30.7e-3;
+WC_V_N2		31.2e-3;
+WC_V_CH4        35e-3; // V_b[cm3/mol]=0.285*V_critical^1.048 (Tyn and Calus; ESTIMATING LIQUID MOLAL VOLUME; Processing, Volume 21, Issue 4, Pages 16 - 17)
+//****** diffusion coeff ***********
+D_H2 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_H2,0.6)"; 
+D_CO2 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_CO2,0.6)"; 
+D_CO #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_CO,0.6)";
+D_CH4 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_CH4,0.6)";
+D_N2 #calc "1.173e-16 * pow($WC_psi * $WC_M,0.5) * $T0 / $muMixLiq / pow($WC_V_N2,0.6)";
+//****** Henry coeff ***************
+H_O2_298 0.032;
+DH_O2   1700;
+H_CO2_298 0.83;
+DH_CO2  2400;
+H_CO_298 0.023;
+DH_CO  1300;
+H_H2_298 0.019;
+DH_H2   500;
+H_CH4_298 0.032;
+DH_CH4   1900;
+H_N2_298 0.015;
+DH_N2   1300;
+He_H2  #calc "$H_H2_298 * exp($DH_H2 *(1. / $T0 - 1./298.15))";
+He_CO  #calc "$H_CO_298 * exp($DH_CO *(1. / $T0 - 1./298.15))";
+He_CO2 #calc "$H_CO2_298 * exp($DH_CO2 *(1. / $T0 - 1./298.15))";
+He_CH4 #calc "$H_CH4_298 * exp($DH_CH4 *(1. / $T0 - 1./298.15))";
+He_N2 #calc "$H_N2_298 * exp($DH_N2 *(1. / $T0 - 1./298.15))";
+//*******inlet gas frac*************
+f_H2 0.1;
+f_CO2 0.9;
+f_N2 0.0;
+//*******inlet gas frac*************
+inletA ;
+liqVol ;
+alphaGas 1;
+alphaLiq 0;
+uGasPhase #calc "$liqVol * $VVM / (60 * $inletA * $alphaGas)";
+//*********************************
+LeLiqH2 #calc "$kThermLiq / $rho0MixLiq / $D_H2 / $CpMixLiq";
+LeLiqCO #calc "$kThermLiq / $rho0MixLiq / $D_CO / $CpMixLiq";
+LeLiqCO2 #calc "$kThermLiq / $rho0MixLiq / $D_CO2 / $CpMixLiq"; // = 74
+LeLiqCH4 #calc "$kThermLiq / $rho0MixLiq / $D_CH4 / $CpMixLiq";
+LeLiqN2 #calc "$kThermLiq / $rho0MixLiq / $D_N2 / $CpMixLiq";
+LeLiqMix #calc "$f_CO2*$LeLiqCO2+$f_H2*$LeLiqH2";
+PrMixLiq #calc "$CpMixLiq * $muMixLiq / $kThermLiq";
+//*********************************
+kH2 #calc "$D_H2*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrH2 #calc "$muMixLiq*$CpMixLiq / $kH2";
+
+kCO #calc "$D_CO*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrCO #calc "$muMixLiq*$CpMixLiq / $kCO";
+
+kCO2 #calc "$D_CO2*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrCO2 #calc "$muMixLiq*$CpMixLiq / $kCO2";
+
+kCH4 #calc "$D_CH4*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrCH4 #calc "$muMixLiq*$CpMixLiq / $kCH4";
+
+kN2 #calc "$D_N2*$rho0MixLiq*$CpMixLiq*$LeLiqMix";
+PrN2 #calc "$muMixLiq*$CpMixLiq / $kN2";
+//*********************************
+l_scale 0.5;
+intensity 0.05;
+k_inlet_gas #calc "1.5 * Foam::pow(($uGasPhase), 2) * Foam::pow($intensity, 2)";
+k_inlet_liq #calc "1.5 * Foam::pow(($uGasPhase), 2) * Foam::pow($intensity, 2)";
+eps_inlet_gas #calc "pow(0.09,0.75) * Foam::pow($k_inlet_gas, 1.5) / ($l_scale * 0.07)";
+eps_inlet_liq #calc "pow(0.09,0.75) * Foam::pow($k_inlet_liq, 1.5) / ($l_scale * 0.07)";
+omega_inlet_gas #calc "pow(0.09,-0.25) * pow($k_inlet_gas,0.5) / ($l_scale * 0.07)";
+omega_inlet_liq #calc "pow(0.09,-0.25) * pow($k_inlet_liq,0.5) / ($l_scale * 0.07)";
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.gas b/papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.gas
new file mode 100644
index 00000000..cca64eef
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.gas
@@ -0,0 +1,26 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      momentumTransport.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+simulationType  laminar;
+//simulationType RAS;
+RAS
+{
+  model  kOmegaSSTSato;
+  turbulence  on;
+  printCoeff  on;
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.liquid b/papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.liquid
new file mode 100644
index 00000000..df3e15b5
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.liquid
@@ -0,0 +1,27 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      momentumTransport.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+//simulationType  laminar;
+simulationType  RAS;
+
+RAS
+{
+    model  kOmegaSSTSato;
+    turbulence      on;
+    printCoeffs     on;
+}
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties b/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties
new file mode 100644
index 00000000..a3c90f5a
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties
@@ -0,0 +1,295 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    object      phaseProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "$FOAM_CASE/constant/globalVars"
+
+type interfaceCompositionPhaseChangePopulationBalanceMultiphaseSystem;
+
+phases (gas liquid);
+
+populationBalances (bubbles);
+
+gas
+{
+    type            multiComponentPhaseModel;//pureIsothermalPhaseModel;
+   
+    diameterModel   velocityGroup;
+
+    velocityGroupCoeffs
+    {
+        populationBalance    bubbles;
+
+        shapeModel           spherical;
+
+        sizeGroups
+        (
+            f1 {dSph  1.4e-3; value 0.0;}
+            f2 {dSph  1.8e-3; value 0.0;}
+            f3 {dSph  2.2e-3; value 0.0;}
+            f4 {dSph  2.6e-3; value 0.0;}
+            f5 {dSph  3e-3; value 1.0;}
+            f6 {dSph  3.4e-3; value 0.0;}
+            f7 {dSph  3.8e-3; value 0.0;}
+            f8 {dSph  4.2e-3; value 0.0;}
+            f9 {dSph  4.6e-3; value 0.0;}
+            f10 {dSph 5.0e-3; value 0.0;}
+        );
+    }
+
+    residualAlpha   1e-6;
+
+    Sc              0.7;
+}
+
+liquid
+{
+    type            multiComponentPhaseModel;//pureIsothermalPhaseModel;
+
+    diameterModel   constant;
+
+    constantCoeffs
+    {
+        d               1e-4;
+    }
+    Sc   #codeStream 
+    { 
+        code 
+        #{ 
+            os  << ($LeLiqMix * $CpMixLiq * $muMixLiq / $kThermLiq); 
+        #}; 
+    }; 
+
+    residualAlpha   1e-6;
+}
+
+populationBalanceCoeffs
+{
+    bubbles
+    {
+        continuousPhase liquid;
+
+        coalescenceModels
+        (
+            LehrMilliesMewes{
+               efficiency 4.695;
+               uCrit 0.08;
+               alphaMax 0.6;
+            }
+        );
+
+        binaryBreakupModels
+        ();
+
+        breakupModels
+        (
+            Laakkonen {
+                efficiency 13.83;
+                daughterSizeDistributionModel Laakkonen;
+            }
+
+        );
+
+        driftModels
+        (
+            densityChange{}
+        );
+
+        nucleationModels
+        ();
+    }
+}
+
+blending
+{
+    default
+    {   
+        type            linear;
+        minFullyContinuousAlpha.gas 0.7;
+        minPartlyContinuousAlpha.gas 0.3;
+        minFullyContinuousAlpha.liquid 0.7;
+        minPartlyContinuousAlpha.liquid 0.3;
+    }
+    heatTransfer
+    {   
+        type            linear;
+        minFullyContinuousAlpha.gas 1;
+        minPartlyContinuousAlpha.gas 0;
+        minFullyContinuousAlpha.liquid 1;
+        minPartlyContinuousAlpha.liquid 0;
+    }
+    massTransfer
+    {
+        $heatTransfer;
+    }
+}
+
+surfaceTension
+(
+    (gas and liquid)
+    {
+        type            constant;
+        sigma           $sigmaLiq;
+    }
+);
+
+interfaceCompression
+();
+
+aspectRatio
+(
+    (gas in liquid)
+    {
+        type            Wellek;
+    }
+);
+
+
+drag
+(
+    (gas in liquid)
+    {
+        type           Grace; // Need to install the model available at https://github.com/NREL/BioReactorDesign
+        //type           IshiiZuber;
+        residualRe 1e-3;
+        swarmCorrection
+        {
+            type        none;
+        }
+    }
+);
+
+virtualMass
+(
+    (gas in liquid)
+    {
+        type            constantCoefficient;
+        Cvm             0.5;
+    }
+);
+
+// heatTransfer
+// ();
+
+heatTransfer.gas
+(
+    (gas in liquid)
+    {
+        type spherical;
+        residualAlpha 1e-4;
+    }
+
+    (liquid in gas)
+    {
+        type RanzMarshall;
+        residualAlpha 1e-4;
+    }
+);
+
+heatTransfer.liquid
+(
+    (gas in liquid)
+    {
+        type RanzMarshall;
+        residualAlpha 1e-4;
+    }
+
+    (liquid in gas)
+    {
+        type spherical;
+        residualAlpha 1e-4;
+    }
+);
+
+interfaceComposition.gas
+();
+
+interfaceComposition.liquid
+(
+    (liquid and gas)
+    {
+        type Henry;
+        species ( CO2 H2 );
+        k ( $He_CO2 $He_H2 );
+        Le $LeLiqMix;
+    }
+);
+
+diffusiveMassTransfer.gas
+();
+
+diffusiveMassTransfer.liquid
+(
+    (gas in liquid)
+    {
+        type Higbie; // Need to install the model available at https://github.com/NREL/BioReactorDesign
+        //type Frossling;
+        Le $LeLiqMix;
+    }
+
+    (liquid in gas)
+    {
+        type spherical;
+        Le 1.0; //not used for spherical
+    }
+);
+
+phaseTransfer
+();
+
+lift
+(
+    (gas in liquid)
+    {
+        type            wallDamped;
+
+        wallDamping
+        {
+            type        cosine;
+            Cd          3.0;
+        }
+
+        lift
+        {
+            type        Tomiyama;
+
+            swarmCorrection
+            {
+                type    none;
+            }
+        }
+    }
+
+);
+
+wallLubrication
+(
+    (gas in liquid)
+    {
+        type            Antal;
+        Cw1             -0.01;
+        Cw2             0.05;
+    }
+);
+
+turbulentDispersion
+(
+    (gas in liquid)
+    {
+        type            Burns;
+        sigma           0.9;
+    }
+);
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_constantd b/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_constantd
new file mode 100644
index 00000000..e029df99
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_constantd
@@ -0,0 +1,261 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    object      phaseProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "$FOAM_CASE/constant/globalVars"
+
+type interfaceCompositionPhaseChangeMultiphaseSystem;
+
+phases (gas liquid);
+
+gas
+{
+    type            multiComponentPhaseModel;//pureIsothermalPhaseModel;
+   
+    diameterModel   constant;
+
+    constantCoeffs
+    {
+        d	3e-3;
+    }
+    residualAlpha   1e-6;
+    Sc              0.7;
+}
+
+liquid
+{
+    type            multiComponentPhaseModel;//pureIsothermalPhaseModel;
+
+    diameterModel   constant;
+
+    constantCoeffs
+    {
+        d               1e-4;
+    }
+    Sc   #codeStream 
+    { 
+        code 
+        #{ 
+            os  << ($LeLiqMix * $CpMixLiq * $muMixLiq / $kThermLiq); 
+        #}; 
+    }; 
+
+    residualAlpha   1e-6;
+}
+
+populationBalanceCoeffs
+{
+    bubbles
+    {
+        continuousPhase liquid;
+
+        coalescenceModels
+        ();
+
+        binaryBreakupModels
+        ();
+
+        breakupModels
+        ();
+
+        driftModels
+        ();
+
+        nucleationModels
+        ();
+    }
+}
+
+blending
+{
+    default
+    {   
+        type            linear;
+        minFullyContinuousAlpha.gas 0.7;
+        minPartlyContinuousAlpha.gas 0.3;
+        minFullyContinuousAlpha.liquid 0.7;
+        minPartlyContinuousAlpha.liquid 0.3;
+    }
+    heatTransfer
+    {   
+        type            linear;
+        minFullyContinuousAlpha.gas 1;
+        minPartlyContinuousAlpha.gas 0;
+        minFullyContinuousAlpha.liquid 1;
+        minPartlyContinuousAlpha.liquid 0;
+    }
+    massTransfer
+    {
+        $heatTransfer;
+    }
+}
+
+surfaceTension
+(
+    (gas and liquid)
+    {
+        type            constant;
+        sigma           $sigmaLiq;
+    }
+);
+
+interfaceCompression
+();
+
+aspectRatio
+(
+    (gas in liquid)
+    {
+        type            Wellek;
+    }
+);
+
+
+drag
+(
+    (gas in liquid)
+    {
+        type           Grace; // Need to install the model available at https://github.com/NREL/BioReactorDesign
+        //type           IshiiZuber;
+        residualRe 1e-3;
+        swarmCorrection
+        {
+            type        none;
+        }
+    }
+);
+
+virtualMass
+(
+    (gas in liquid)
+    {
+        type            constantCoefficient;
+        Cvm             0.5;
+    }
+);
+
+// heatTransfer
+// ();
+
+heatTransfer.gas
+(
+    (gas in liquid)
+    {
+        type spherical;
+        residualAlpha 1e-4;
+    }
+
+    (liquid in gas)
+    {
+        type RanzMarshall;
+        residualAlpha 1e-4;
+    }
+);
+
+heatTransfer.liquid
+(
+    (gas in liquid)
+    {
+        type RanzMarshall;
+        residualAlpha 1e-4;
+    }
+
+    (liquid in gas)
+    {
+        type spherical;
+        residualAlpha 1e-4;
+    }
+);
+
+interfaceComposition.gas
+();
+
+interfaceComposition.liquid
+(
+    (liquid and gas)
+    {
+        type Henry;
+        species ( CO2 H2 );
+        k ( $He_CO2 $He_H2 );
+        Le $LeLiqMix;
+    }
+);
+
+diffusiveMassTransfer.gas
+();
+
+diffusiveMassTransfer.liquid
+(
+    (gas in liquid)
+    {
+        type Higbie; // Need to install the model available at https://github.com/NREL/BioReactorDesign
+        //type Frossling;
+        Le $LeLiqMix;
+    }
+
+    (liquid in gas)
+    {
+        type spherical;
+        Le 1.0; //not used for spherical
+    }
+);
+
+phaseTransfer
+();
+
+lift
+(
+    (gas in liquid)
+    {
+        type            wallDamped;
+
+        wallDamping
+        {
+            type        cosine;
+            Cd          3.0;
+        }
+
+        lift
+        {
+            type        Tomiyama;
+
+            swarmCorrection
+            {
+                type    none;
+            }
+        }
+    }
+
+);
+
+wallLubrication
+(
+    (gas in liquid)
+    {
+        type            Antal;
+        Cw1             -0.01;
+        Cw2             0.05;
+    }
+);
+
+turbulentDispersion
+(
+    (gas in liquid)
+    {
+        type            Burns;
+        sigma           0.9;
+    }
+);
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_pbe b/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_pbe
new file mode 100644
index 00000000..a3c90f5a
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_pbe
@@ -0,0 +1,295 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  9
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    object      phaseProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "$FOAM_CASE/constant/globalVars"
+
+type interfaceCompositionPhaseChangePopulationBalanceMultiphaseSystem;
+
+phases (gas liquid);
+
+populationBalances (bubbles);
+
+gas
+{
+    type            multiComponentPhaseModel;//pureIsothermalPhaseModel;
+   
+    diameterModel   velocityGroup;
+
+    velocityGroupCoeffs
+    {
+        populationBalance    bubbles;
+
+        shapeModel           spherical;
+
+        sizeGroups
+        (
+            f1 {dSph  1.4e-3; value 0.0;}
+            f2 {dSph  1.8e-3; value 0.0;}
+            f3 {dSph  2.2e-3; value 0.0;}
+            f4 {dSph  2.6e-3; value 0.0;}
+            f5 {dSph  3e-3; value 1.0;}
+            f6 {dSph  3.4e-3; value 0.0;}
+            f7 {dSph  3.8e-3; value 0.0;}
+            f8 {dSph  4.2e-3; value 0.0;}
+            f9 {dSph  4.6e-3; value 0.0;}
+            f10 {dSph 5.0e-3; value 0.0;}
+        );
+    }
+
+    residualAlpha   1e-6;
+
+    Sc              0.7;
+}
+
+liquid
+{
+    type            multiComponentPhaseModel;//pureIsothermalPhaseModel;
+
+    diameterModel   constant;
+
+    constantCoeffs
+    {
+        d               1e-4;
+    }
+    Sc   #codeStream 
+    { 
+        code 
+        #{ 
+            os  << ($LeLiqMix * $CpMixLiq * $muMixLiq / $kThermLiq); 
+        #}; 
+    }; 
+
+    residualAlpha   1e-6;
+}
+
+populationBalanceCoeffs
+{
+    bubbles
+    {
+        continuousPhase liquid;
+
+        coalescenceModels
+        (
+            LehrMilliesMewes{
+               efficiency 4.695;
+               uCrit 0.08;
+               alphaMax 0.6;
+            }
+        );
+
+        binaryBreakupModels
+        ();
+
+        breakupModels
+        (
+            Laakkonen {
+                efficiency 13.83;
+                daughterSizeDistributionModel Laakkonen;
+            }
+
+        );
+
+        driftModels
+        (
+            densityChange{}
+        );
+
+        nucleationModels
+        ();
+    }
+}
+
+blending
+{
+    default
+    {   
+        type            linear;
+        minFullyContinuousAlpha.gas 0.7;
+        minPartlyContinuousAlpha.gas 0.3;
+        minFullyContinuousAlpha.liquid 0.7;
+        minPartlyContinuousAlpha.liquid 0.3;
+    }
+    heatTransfer
+    {   
+        type            linear;
+        minFullyContinuousAlpha.gas 1;
+        minPartlyContinuousAlpha.gas 0;
+        minFullyContinuousAlpha.liquid 1;
+        minPartlyContinuousAlpha.liquid 0;
+    }
+    massTransfer
+    {
+        $heatTransfer;
+    }
+}
+
+surfaceTension
+(
+    (gas and liquid)
+    {
+        type            constant;
+        sigma           $sigmaLiq;
+    }
+);
+
+interfaceCompression
+();
+
+aspectRatio
+(
+    (gas in liquid)
+    {
+        type            Wellek;
+    }
+);
+
+
+drag
+(
+    (gas in liquid)
+    {
+        type           Grace; // Need to install the model available at https://github.com/NREL/BioReactorDesign
+        //type           IshiiZuber;
+        residualRe 1e-3;
+        swarmCorrection
+        {
+            type        none;
+        }
+    }
+);
+
+virtualMass
+(
+    (gas in liquid)
+    {
+        type            constantCoefficient;
+        Cvm             0.5;
+    }
+);
+
+// heatTransfer
+// ();
+
+heatTransfer.gas
+(
+    (gas in liquid)
+    {
+        type spherical;
+        residualAlpha 1e-4;
+    }
+
+    (liquid in gas)
+    {
+        type RanzMarshall;
+        residualAlpha 1e-4;
+    }
+);
+
+heatTransfer.liquid
+(
+    (gas in liquid)
+    {
+        type RanzMarshall;
+        residualAlpha 1e-4;
+    }
+
+    (liquid in gas)
+    {
+        type spherical;
+        residualAlpha 1e-4;
+    }
+);
+
+interfaceComposition.gas
+();
+
+interfaceComposition.liquid
+(
+    (liquid and gas)
+    {
+        type Henry;
+        species ( CO2 H2 );
+        k ( $He_CO2 $He_H2 );
+        Le $LeLiqMix;
+    }
+);
+
+diffusiveMassTransfer.gas
+();
+
+diffusiveMassTransfer.liquid
+(
+    (gas in liquid)
+    {
+        type Higbie; // Need to install the model available at https://github.com/NREL/BioReactorDesign
+        //type Frossling;
+        Le $LeLiqMix;
+    }
+
+    (liquid in gas)
+    {
+        type spherical;
+        Le 1.0; //not used for spherical
+    }
+);
+
+phaseTransfer
+();
+
+lift
+(
+    (gas in liquid)
+    {
+        type            wallDamped;
+
+        wallDamping
+        {
+            type        cosine;
+            Cd          3.0;
+        }
+
+        lift
+        {
+            type        Tomiyama;
+
+            swarmCorrection
+            {
+                type    none;
+            }
+        }
+    }
+
+);
+
+wallLubrication
+(
+    (gas in liquid)
+    {
+        type            Antal;
+        Cw1             -0.01;
+        Cw2             0.05;
+    }
+);
+
+turbulentDispersion
+(
+    (gas in liquid)
+    {
+        type            Burns;
+        sigma           0.9;
+    }
+);
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.gas b/papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.gas
new file mode 100644
index 00000000..11b1c4b9
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.gas
@@ -0,0 +1,142 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      thermophysicalProperties.gas;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+thermoType
+{
+    type            heRhoThermo;
+    mixture         multiComponentMixture;
+    transport       sutherland;
+    thermo          janaf;
+    equationOfState perfectGas;
+    specie          specie;
+    energy          sensibleInternalEnergy;
+    //energy          sensibleEnthalpy;
+}
+
+
+species
+(
+    H2
+    CO2
+    N2
+);
+
+defaultSpecie N2;
+
+CO2
+{
+    specie
+    {
+        molWeight       44.00995;
+    }
+    thermodynamics
+    {
+        Tlow            200;
+        Thigh           3500;
+        Tcommon         1000;
+        highCpCoeffs    ( 3.85746029 0.00441437026 -2.21481404e-06 5.23490188e-10 -4.72084164e-14 -48759.166 2.27163806 );
+        lowCpCoeffs     ( 2.35677352 0.00898459677 -7.12356269e-06 2.45919022e-09 -1.43699548e-13 -48371.9697 9.90105222 );
+    }
+    transport
+    {
+        As              1.572e-06;
+        Ts              240;
+    }
+    elements
+    {
+        C               1;
+        O               2;
+    }
+}
+
+water
+{
+    specie
+    {
+        molWeight       18.01534;
+    }
+    thermodynamics
+    {
+        Tlow            200;
+        Thigh           3500;
+        Tcommon         1000;
+        highCpCoeffs    ( 3.03399249 0.00217691804 -1.64072518e-07 -9.7041987e-11 1.68200992e-14 -30004.2971 4.9667701 );
+        lowCpCoeffs     ( 4.19864056 -0.0020364341 6.52040211e-06 -5.48797062e-09 1.77197817e-12 -30293.7267 -0.849032208 );
+    }
+    transport
+    {
+        As              1.512e-06;
+        Ts              120;
+    }
+    elements
+    {
+        H               2;
+        O               1;
+    }
+}
+
+N2
+{
+    specie
+    {
+        molWeight       28.0134;
+    }
+    thermodynamics
+    {
+        Tlow            250;
+        Thigh           5000;
+        Tcommon         1000;
+        highCpCoeffs    ( 2.92664 0.0014879768 -5.68476e-07 1.0097038e-10 -6.753351e-15 -922.7977 5.980528 );
+        lowCpCoeffs     ( 3.298677 0.0014082404 -3.963222e-06 5.641515e-09 -2.444854e-12 -1020.8999 3.950372 );
+    }
+    transport
+    {
+        As              1.512e-06;
+        Ts              120;
+    }
+    elements
+    {
+        N               2;
+    }
+}
+
+H2
+{
+    specie
+    {
+        molWeight       2.01594;
+    }
+    thermodynamics
+    {
+        Tlow            200;
+        Thigh           3500;
+        Tcommon         1000;
+        highCpCoeffs    ( 3.3372792 -4.94024731e-05 4.99456778e-07 -1.79566394e-10 2.00255376e-14 -950.158922 -3.20502331 );
+        lowCpCoeffs     ( 2.34433112 0.00798052075 -1.9478151e-05 2.01572094e-08 -7.37611761e-12 -917.935173 0.683010238 );
+    }
+    transport
+    {
+        As              6.362e-07;
+        Ts              72;
+    }
+    elements
+    {
+        H               2;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.liquid b/papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.liquid
new file mode 100644
index 00000000..d324ec51
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.liquid
@@ -0,0 +1,108 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      thermophysicalProperties.liquid;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "$FOAM_CASE/constant/globalVars"
+
+thermoType
+{
+    type            heRhoThermo;
+    mixture         multiComponentMixture;
+    transport       const;
+    thermo          hConst;
+    equationOfState rhoConst;//rPolynomial;
+    specie          specie;
+    energy          sensibleInternalEnergy;
+    //energy          sensibleEnthalpy;
+}
+
+species
+(
+    CO2
+    water
+    H2
+);
+
+inertSpecie water;
+
+water
+{
+    specie
+    {
+        molWeight   18.0153;
+    }
+    equationOfState
+    {
+        rho     $rho0MixLiq;
+    }
+    thermodynamics
+    {
+        Cp          $CpMixLiq;
+        Hf          -1.5879e+07;
+    }
+    transport
+    {
+        mu          $muMixLiq;
+        Pr          $PrMixLiq;
+    }
+}
+
+CO2 
+{   
+    specie
+    {   
+        molWeight   44.00995;
+    }
+    equationOfState
+    {
+        rho     $rho0MixLiq;
+    }
+    thermodynamics
+    {   
+        Cp          $CpMixLiq;
+        Hf         -1.5879e+07;
+    }
+    transport           
+    {   
+        mu          $muMixLiq;
+        Pr          $PrCO2;
+    }   
+} 
+
+H2
+{
+    specie
+    {
+        molWeight   2.01594;
+    }
+    equationOfState
+    {
+        rho     $rho0MixLiq;
+    }
+    thermodynamics
+    {
+        Cp          $CpMixLiq;
+        Hf         -1.5879e+07;//-9402451;
+    }
+    transport
+    {
+        mu          $muMixLiq;
+        Pr          $PrH2;
+    }
+}
+
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/get_qoi.py b/papers/scaleup/generate_scaleup_runs/template/get_qoi.py
new file mode 100644
index 00000000..6c06e054
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/get_qoi.py
@@ -0,0 +1,227 @@
+import json
+import os
+import pickle as pkl
+
+import matplotlib as mpl
+import numpy as np
+from prettyPlot.plotting import *
+from scipy.optimize import curve_fit
+
+
+def get_sim_folds(path):
+    folds = os.listdir(path)
+    sim_folds = []
+    for fold in folds:
+        if fold.startswith("loop"):
+            sim_folds.append(fold)
+    return sim_folds
+
+
+def func(t, cstar, kla):
+    t = t
+    t0 = 0
+    c0 = 0
+    return (cstar - c0) * (1 - np.exp(-kla * (t - t0))) + c0
+
+
+def get_vl(verb=False):
+    filename = os.path.join("constant", "globalVars")
+    with open(filename, "r+") as f:
+        lines = f.readlines()
+    for line in lines:
+        if line.startswith("liqVol"):
+            vol = float(line.split()[-1][:-1])
+            break
+    if verb:
+        print(f"Read liqVol = {vol}m3")
+    return vol
+
+
+def get_vvm(verb=False):
+    filename = os.path.join("constant", "globalVars")
+    with open(filename, "r+") as f:
+        lines = f.readlines()
+    for line in lines:
+        if line.startswith("VVM"):
+            vvm = float(line.split()[-1][:-1])
+            break
+    if verb:
+        print(f"Read VVM = {vvm} [-]")
+    return vvm
+
+
+def get_As(verb=False):
+    filename = os.path.join("constant", "globalVars")
+    with open(filename, "r+") as f:
+        lines = f.readlines()
+    for line in lines:
+        if line.startswith("inletA"):
+            As = float(line.split()[-1][:-1])
+            break
+    if verb:
+        print(f"Read As = {As}m2")
+    return As
+
+
+def get_pmix(verb=False):
+    with open("system/mixers.json", "r+") as f:
+        data = json.load(f)
+    mixer_list = data["mixers"]
+    pmix = 0
+    for mix in mixer_list:
+        pmix += mix["power"] / 1000
+    if verb:
+        print(f"Read Mixing power = {pmix}kW")
+    return pmix
+
+
+def get_lh(verb=False):
+    filename = os.path.join("system", "setFieldsDict")
+    with open(filename, "r+") as f:
+        lines = f.readlines()
+    for line in lines:
+        if "box (-1.0 -1.0 -1.0)" in line:
+            height = float(line.split("(")[2].split()[1])
+            break
+    if verb:
+        print(f"Read Height = {height}m")
+    return height
+
+
+def get_pinj(vvm, Vl, As, lh):
+    rhog = 0.593333  # kg /m3
+    Vg = Vl * vvm / (60 * As * 1)  # m/s
+    Ptank = 101325  # Pa
+    # Ptank = 0 # Pa
+    rhoL = 1000  # kg / m3
+    Pl = 101325 + rhoL * 9.8 * lh  # Pa
+    # W
+    P1 = rhog * As * Vg**3
+    # W
+    P2 = (Pl - Ptank) * As * Vg
+    # kg /s
+    MF = rhog * Vg * As
+    # kwh / kg
+    e_m = (P1 + P2) / (3600 * 1000 * MF)
+
+    # returns kW
+    return (P1 + P2) * 1e-3
+
+
+def get_qoi(kla_co2, cs_co2, kla_h2, cs_h2, verb=False):
+    vvm = get_vvm(verb)
+    As = get_As(verb)
+    V_l = get_vl(verb)
+    liqh = get_lh(verb)
+    P_inj = get_pinj(vvm, V_l, As, liqh)
+    P_mix = get_pmix(verb)
+
+    qoi_kla_co2 = kla_co2 * cs_co2 * V_l * 0.04401
+    qoi_kla_h2 = kla_h2 * cs_h2 * V_l * 0.002016
+
+    qoi_co2 = qoi_kla_co2 / (P_mix / 3600 + P_inj / 3600)
+    qoi_h2 = qoi_kla_h2 / (P_mix / 3600 + P_inj / 3600)
+    return (
+        qoi_co2 * qoi_h2,
+        qoi_kla_co2 * qoi_kla_h2,
+        qoi_co2 + qoi_h2,
+        qoi_kla_co2 + qoi_kla_h2,
+    )
+
+
+def get_qoi_uq(kla_co2, cs_co2, kla_h2, cs_h2):
+    qoi = []
+    qoi_kla = []
+    qoi_sum = []
+    qoi_sum_kla = []
+    for i in range(len(kla_co2)):
+        if i == 0:
+            verb = True
+        else:
+            verb = False
+        qoi_tmp, qoi_kla_tmp, qoi_sum_tmp, qoi_sum_kla_tmp = get_qoi(
+            kla_co2[i], cs_co2[i], kla_h2[i], cs_h2[i], verb
+        )
+        qoi.append(qoi_tmp)
+        qoi_kla.append(qoi_kla_tmp)
+        qoi_sum.append(qoi_sum_tmp)
+        qoi_sum_kla.append(qoi_sum_kla_tmp)
+    qoi = np.array(qoi)
+    qoi_kla = np.array(qoi_kla)
+    qoi_sum = np.array(qoi_sum)
+    qoi_sum_kla = np.array(qoi_sum_kla)
+    return (
+        np.mean(qoi),
+        np.std(qoi),
+        np.mean(qoi_kla),
+        np.std(qoi_kla),
+        np.mean(qoi_sum),
+        np.std(qoi_sum),
+        np.mean(qoi_sum_kla),
+        np.std(qoi_sum_kla),
+    )
+
+
+os.makedirs("Figures", exist_ok=True)
+
+dataFolder = "data"
+fold = "local"
+
+nuq = 100
+mean_cstar_co2 = np.random.uniform(7.68, 8.22, nuq)
+mean_cstar_h2 = np.random.uniform(0.516, 0.548, nuq)
+
+
+tmp_cs_h2 = []
+tmp_cs_co2 = []
+tmp_kla_h2 = []
+tmp_kla_co2 = []
+cs_co2 = mean_cstar_co2
+cs_h2 = mean_cstar_h2
+
+a = np.load(os.path.join(dataFolder, fold, "conv.npz"))
+endindex = -1
+if (
+    "c_h2" in a
+    and "c_co2" in a
+    and len(a["time"][:endindex] > 0)
+    and (a["time"][:endindex][-1] > 85)
+):
+    for i in range(nuq):
+        fitparamsH2, _ = curve_fit(
+            func,
+            np.array(a["time"][:endindex]),
+            np.array(a["c_h2"][:endindex]),
+            bounds=[(cs_h2[i] - 1e-6, 0), (cs_h2[i] + 1e-6, 1)],
+        )
+        fitparamsCO2, _ = curve_fit(
+            func,
+            np.array(a["time"][:endindex]),
+            np.array(a["c_co2"][:endindex]),
+            bounds=[(cs_co2[i] - 1e-6, 0), (cs_co2[i] + 1e-6, 1)],
+        )
+        tmp_kla_co2.append(fitparamsCO2[1])
+        tmp_kla_h2.append(fitparamsH2[1])
+        tmp_cs_h2.append(cs_h2[i])
+        tmp_cs_co2.append(cs_co2[i])
+
+(
+    qoi_m,
+    qoi_s,
+    qoi_kla_m,
+    qoi_kla_s,
+    qoi_sum_m,
+    qoi_sum_s,
+    qoi_sum_kla_m,
+    qoi_sum_kla_s,
+) = get_qoi_uq(tmp_kla_co2, tmp_cs_co2, tmp_kla_h2, tmp_cs_h2)
+
+
+with open("qoi.txt", "w+") as f:
+    f.write(f"{qoi_m},{qoi_s}\n")
+with open("qoi_kla.txt", "w+") as f:
+    f.write(f"{qoi_kla_m},{qoi_kla_s}\n")
+with open("qoi_sum.txt", "w+") as f:
+    f.write(f"{qoi_sum_m},{qoi_sum_s}\n")
+with open("qoi_sum_kla.txt", "w+") as f:
+    f.write(f"{qoi_sum_kla_m},{qoi_sum_kla_s}\n")
diff --git a/papers/scaleup/generate_scaleup_runs/template/presteps.sh b/papers/scaleup/generate_scaleup_runs/template/presteps.sh
new file mode 100644
index 00000000..d47dfe51
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/presteps.sh
@@ -0,0 +1,75 @@
+# Clean case
+module load conda
+#conda activate /projects/gas2fuels/conda_env/bird_wf
+conda activate /projects/gas2fuels/conda_env/bird_mixer
+source /projects/gas2fuels/ofoam_cray_mpich/OpenFOAM-dev/etc/bashrc
+./Allclean
+
+BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR)"`
+
+echo PRESTEP 1
+# Generate blockmeshDict
+python ${BIRD_HOME}/../applications/write_block_rect_mesh.py -i system/mesh.json -o system
+
+# Generate boundary stl
+python ${BIRD_HOME}/../applications/write_stl_patch.py -i system/inlets_outlets.json
+
+# Generate mixers
+python ${BIRD_HOME}/../applications/write_dynMix_fvModels.py -fs -i system/mixers.json -o constant
+
+echo PRESTEP 2
+# Mesh gen
+blockMesh -dict system/blockMeshDict
+
+mkdir tmp
+
+# Inlet BC
+surfaceToPatch -tol 1e-3 inlets.stl
+export newmeshdir=$(foamListTimes -latestTime)
+rm -rf constant/polyMesh/
+cp -r $newmeshdir/polyMesh ./constant
+rm -rf $newmeshdir
+cp constant/polyMesh/boundary tmp
+sed -i -e 's/inlets\.stl/inlet/g' tmp/boundary
+cat tmp/boundary > constant/polyMesh/boundary
+
+# Outlet BC
+surfaceToPatch -tol 1e-3 outlets.stl
+export newmeshdir=$(foamListTimes -latestTime)
+rm -rf constant/polyMesh/
+cp -r $newmeshdir/polyMesh ./constant
+rm -rf $newmeshdir
+cp constant/polyMesh/boundary tmp
+sed -i -e 's/outlets\.stl/outlet/g' tmp/boundary
+cat tmp/boundary > constant/polyMesh/boundary
+
+
+rm -r tmp
+
+# Scale
+transformPoints "scale=(2.7615275385627096 2.7615275385627096 2.7615275385627096)"
+
+
+# setup IC
+cp -r 0.orig 0
+setFields
+
+# Setup mass flow rate
+# Get inlet area
+postProcess -func 'patchIntegrate(patch="inlet", field="alpha.gas")'
+postProcess -func writeCellVolumes
+writeMeshObj
+
+echo PRESTEP 3
+python writeGlobalVars.py
+cp constant/phaseProperties_constantd constant/phaseProperties
+
+conda deactivate
+
+if [ -f qoi.txt ]; then
+    rm qoi.txt
+fi
+if [ -f data/local/conv.npz ]; then
+    rm data/local/conv.npz
+fi
+
diff --git a/papers/scaleup/generate_scaleup_runs/template/read_history.py b/papers/scaleup/generate_scaleup_runs/template/read_history.py
new file mode 100644
index 00000000..0ca46649
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/read_history.py
@@ -0,0 +1,100 @@
+import argparse
+import os
+import sys
+
+import numpy as np
+from prettyPlot.plotting import plt, pretty_labels
+
+from bird.postprocess.post_quantities import *
+from bird.utilities.ofio import *
+
+parser = argparse.ArgumentParser(description="Convergence of GH")
+parser.add_argument(
+    "-cn",
+    "--case_name",
+    type=str,
+    metavar="",
+    required=True,
+    help="Case name",
+)
+parser.add_argument(
+    "-df",
+    "--data_folder",
+    type=str,
+    metavar="",
+    required=False,
+    help="data folder name",
+    default="data",
+)
+
+args, unknown = parser.parse_known_args()
+
+
+case_root = "."  # "../"
+case_name = args.case_name  # "12_hole_sparger_snappyRefine_700rpm_opt_coeff"
+case_folder = "."
+dataFolder = args.data_folder
+
+if os.path.isfile(os.path.join(dataFolder, case_name, "conv.npz")):
+    sys.exit("WARNING: History already created, Skipping")
+
+time_float_sorted, time_str_sorted = get_case_times(
+    case_folder, remove_zero=True
+)
+cell_centers, _ = read_cell_centers(case_folder)
+nCells = len(cell_centers)
+
+
+co2_history = np.zeros(len(time_str_sorted))
+c_co2_history = np.zeros(len(time_str_sorted))
+h2_history = np.zeros(len(time_str_sorted))
+c_h2_history = np.zeros(len(time_str_sorted))
+gh_history = np.zeros(len(time_str_sorted))
+liqvol_history = np.zeros(len(time_str_sorted))
+print(f"case_folder = {case_folder}")
+field_dict = {}
+for itime, time in enumerate(time_float_sorted):
+    time_folder = time_str_sorted[itime]
+    print(f"\tTime : {time_folder}")
+    _, field_dict = read_cell_volumes(case_folder)
+    gh_history[itime], field_dict = compute_gas_holdup(
+        case_folder,
+        time_str_sorted[itime],
+        field_dict=field_dict,
+    )
+    co2_history[itime], field_dict = compute_ave_y_liq(
+        case_folder,
+        time_str_sorted[itime],
+        species_name="CO2",
+        field_dict=field_dict,
+    )
+    h2_history[itime], field_dict = compute_ave_y_liq(
+        case_folder,
+        time_str_sorted[itime],
+        species_name="H2",
+        field_dict=field_dict,
+    )
+    c_co2_history[itime], field_dict = compute_ave_conc_liq(
+        case_folder,
+        time_str_sorted[itime],
+        species_name="CO2",
+        field_dict=field_dict,
+    )
+    c_h2_history[itime], field_dict = compute_ave_conc_liq(
+        case_folder,
+        time_str_sorted[itime],
+        species_name="H2",
+        field_dict=field_dict,
+    )
+
+os.makedirs(dataFolder, exist_ok=True)
+os.makedirs(os.path.join(dataFolder, case_name), exist_ok=True)
+np.savez(
+    os.path.join(dataFolder, case_name, "conv.npz"),
+    time=np.array(time_float_sorted),
+    gh=gh_history,
+    co2=co2_history,
+    h2=h2_history,
+    c_h2=c_h2_history,
+    c_co2=c_co2_history,
+)
diff --git a/papers/scaleup/generate_scaleup_runs/template/run.sh b/papers/scaleup/generate_scaleup_runs/template/run.sh
new file mode 100644
index 00000000..99da4760
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/run.sh
@@ -0,0 +1,5 @@
+birdmultiphaseEulerFoam
+
+
+
+
diff --git a/papers/scaleup/generate_scaleup_runs/template/script b/papers/scaleup/generate_scaleup_runs/template/script
new file mode 100755
index 00000000..efe675ff
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/script
@@ -0,0 +1,14 @@
+#!/bin/bash
+#SBATCH --qos=high
+#SBATCH --job-name=val2
+##SBATCH --partition=debug
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=16
+#SBATCH --time=07:59:00
+#SBATCH --account=co2snow
+
+bash presteps.sh
+source /projects/gas2fuels/ofoam_cray_mpich/OpenFOAM-dev/etc/bashrc
+decomposePar -fileHandler collated
+srun -n 16 birdmultiphaseEulerFoam -parallel -fileHandler collated
+reconstructPar -newTimes
diff --git a/papers/scaleup/generate_scaleup_runs/template/script_post b/papers/scaleup/generate_scaleup_runs/template/script_post
new file mode 100755
index 00000000..aabbc33e
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/script_post
@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --qos=high
+#SBATCH --job-name=val2
+##SBATCH --partition=debug
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=16
+#SBATCH --time=00:59:00
+#SBATCH --account=co2snow
+
+bash computeQOI.sh
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/blockMeshDict b/papers/scaleup/generate_scaleup_runs/template/system/blockMeshDict
new file mode 100644
index 00000000..1183d262
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/blockMeshDict
@@ -0,0 +1,746 @@
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+
+convertToMeters 1.0;
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+vertices
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+);
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+blocks
+(
+
+ //block 0
+hex (0 1 12 11 88 89 100 99 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 1
+hex (1 2 13 12 89 90 101 100 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 2
+hex (2 3 14 13 90 91 102 101 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 3
+hex (3 4 15 14 91 92 103 102 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 4
+hex (4 5 16 15 92 93 104 103 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 5
+hex (5 6 17 16 93 94 105 104 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 6
+hex (6 7 18 17 94 95 106 105 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 7
+hex (7 8 19 18 95 96 107 106 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 8
+hex (8 9 20 19 96 97 108 107 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 9
+hex (9 10 21 20 97 98 109 108 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 10
+hex (97 98 109 108 185 186 197 196 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 11
+hex (185 186 197 196 273 274 285 284 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 12
+hex (273 274 285 284 361 362 373 372 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 13
+hex (361 362 373 372 449 450 461 460 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 14
+hex (360 361 372 371 448 449 460 459 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 15
+hex (359 360 371 370 447 448 459 458 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 16
+hex (358 359 370 369 446 447 458 457 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 17
+hex (357 358 369 368 445 446 457 456 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 18
+hex (356 357 368 367 444 445 456 455 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 19
+hex (355 356 367 366 443 444 455 454 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 20
+hex (354 355 366 365 442 443 454 453 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 21
+hex (353 354 365 364 441 442 453 452 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 22
+hex (352 353 364 363 440 441 452 451 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 23
+hex (363 364 375 374 451 452 463 462 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 24
+hex (374 375 386 385 462 463 474 473 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 25
+hex (385 386 397 396 473 474 485 484 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 26
+hex (396 397 408 407 484 485 496 495 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 27
+hex (407 408 419 418 495 496 507 506 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 28
+hex (418 419 430 429 506 507 518 517 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 29
+hex (308 309 320 319 396 397 408 407 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 30
+hex (220 221 232 231 308 309 320 319 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 31
+hex (132 133 144 143 220 221 232 231 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 32
+hex (44 45 56 55 132 133 144 143 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 33
+hex (55 56 67 66 143 144 155 154 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 34
+hex (66 67 78 77 154 155 166 165 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 35
+hex (33 34 45 44 121 122 133 132 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 36
+hex (22 23 34 33 110 111 122 121 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+
+ //block 37
+hex (11 12 23 22 99 100 111 110 )
+( 10 10 10 )
+SimpleGrading (1 1 1)
+);
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+defaultPatch
+{   type wall;}
+
+patches
+(
+);
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/controlDict b/papers/scaleup/generate_scaleup_runs/template/system/controlDict
new file mode 100644
index 00000000..7561264c
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/controlDict
@@ -0,0 +1,67 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     birdmultiphaseEulerFoam;
+
+startFrom       latestTime;//startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         200;
+
+deltaT          0.0001;
+
+writeControl    adjustableRunTime;
+
+writeInterval   2;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  6;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable yes;
+
+adjustTimeStep  yes;
+
+maxCo           0.25;
+
+maxDeltaT       0.005;
+
+
+functions
+{
+
+    #includeFunc    writeObjects(d.gas)
+    #includeFunc    writeObjects(thermo:rho.gas)
+    #includeFunc    writeObjects(thermo:rho.liquid)
+}
+//functions
+//{
+//    #includeFunc fieldAverage(U.air, U.water, alpha.air, p)
+//}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/decomposeParDict b/papers/scaleup/generate_scaleup_runs/template/system/decomposeParDict
new file mode 100755
index 00000000..f8397e73
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/decomposeParDict
@@ -0,0 +1,30 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  3.0.x                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberOfSubdomains 16;
+
+method          scotch;
+
+hierarchicalCoeffs
+{
+    n               (4 4 1);
+    delta           0.001;
+    order           xyz;
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/fvConstraints b/papers/scaleup/generate_scaleup_runs/template/system/fvConstraints
new file mode 100644
index 00000000..334f1c8f
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/fvConstraints
@@ -0,0 +1,56 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    object      fvConstraints;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+limitp
+{
+    type       limitPressure;
+
+    min        1e4;
+}
+limitUliq
+{
+    type       limitVelocity;
+    active yes;
+    U          U.liquid;
+    selectionMode all;
+    max        1e1;
+}
+limitUgas
+{
+    type       limitVelocity;
+    active yes;
+    U          U.gas;
+    selectionMode all;
+    max        2e1;
+}
+limitTgas
+{
+    type            limitTemperature;
+    selectionMode   all;
+    min             290;
+    max             310;
+    phase           gas;
+}
+limitTliq
+{
+    type            limitTemperature;
+    selectionMode   all;
+    min             290;
+    max             310;
+    phase           liquid;
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/fvSchemes b/papers/scaleup/generate_scaleup_runs/template/system/fvSchemes
new file mode 100644
index 00000000..9e5fed8b
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/fvSchemes
@@ -0,0 +1,70 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+    default         Euler;
+}
+
+gradSchemes
+{
+    default         Gauss linear;
+    limited         cellLimited Gauss linear 1;
+}
+
+divSchemes
+{
+    default                     none;
+
+    "div\(phi,alpha.*\)"              Gauss vanLeer;
+
+    "div\(phir,alpha.*,alpha.*\)"       Gauss vanLeer;
+
+    "div\(alphaRhoPhi.*,U.*\)"          Gauss limitedLinearV 1;
+    "div\(phi.*,U.*\)"                  Gauss limitedLinearV 1;
+    "div\(alphaRhoPhi.*,Yi\)"       Gauss limitedLinear 1;
+    "div\(alphaRhoPhi.*,(h|e).*\)"          Gauss limitedLinear 1;
+    "div\(alphaRhoPhi.*,(K|k|epsilon|omega).*\)"          Gauss limitedLinear 1;
+    "div\(alphaPhi.*,f.*\)"         Gauss limitedLinear 1;
+    "div\(alphaRhoPhi.*,\(p\|thermo:rho.*\)\)"    Gauss limitedLinear 1;
+
+    "div\(phim,(k|epsilon|omega)m\)"      Gauss upwind;
+    "div\(\(\(\(alpha.*\*thermo:rho.*\)*nuEff.*\)*dev2\(T\(grad\(U.*\)\)\)\)\)" Gauss linear;
+}
+
+laplacianSchemes
+{
+    default         Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+    default         linear;
+}
+
+snGradSchemes
+{
+    default         uncorrected;
+}
+
+wallDist
+{
+    method          Poisson;
+    nRequired       true;
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/fvSolution b/papers/scaleup/generate_scaleup_runs/template/system/fvSolution
new file mode 100644
index 00000000..05d80e1e
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/fvSolution
@@ -0,0 +1,121 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+    "alpha.*"
+    {
+        nAlphaCorr      2;
+        nAlphaSubCycles 5;
+    }
+
+    bubbles
+    {
+        nCorr                1;
+        tolerance            1e-4;
+        scale                true;
+        solveOnFinalIterOnly true;
+        sourceUpdateInterval 1;
+    }
+
+    p_rgh
+    {
+        solver          GAMG;
+        smoother        DIC;
+        tolerance       1e-7;
+        relTol          0;
+    }
+
+    p_rghFinal
+    {
+        $p_rgh;
+        relTol          0;
+    }
+
+    "(k|omega|epsilon).*"
+    {
+        solver          smoothSolver;
+        smoother        symGaussSeidel;
+        tolerance       1e-7;
+        relTol          1e-4;
+        minIter         0;
+        maxIter         3;
+    }
+
+    "(e|h).*"
+    {
+        solver          smoothSolver;
+        smoother        symGaussSeidel;
+        tolerance       1e-8;
+        relTol          0;
+        minIter         0;
+        maxIter         3;
+    }
+
+    "f.*"
+    {
+        solver          PBiCGStab;
+        preconditioner  DILU;
+        tolerance       1e-6;
+        relTol          0;
+    }
+
+    "Yi.*"
+    {
+        solver          PBiCGStab;
+        preconditioner  DILU;
+        tolerance       1e-12;
+        relTol          0;
+        residualAlpha   1e-8;
+    }
+
+    "U.*"
+    {
+        solver          smoothSolver;
+        smoother        symGaussSeidel;
+        tolerance       1e-5;
+        relTol          0;
+        minIter         1;
+    }
+
+    yPsi
+    {
+        solver          PCG;
+        preconditioner  DIC;
+        tolerance       1e-10;
+        relTol          0;
+    }
+
+}
+
+PIMPLE
+{
+    nOuterCorrectors 3;
+    nCorrectors      1;
+    nNonOrthogonalCorrectors 0;
+
+}
+
+relaxationFactors
+{
+    equations
+    {
+        ".*"            1;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/inlets_outlets.json b/papers/scaleup/generate_scaleup_runs/template/system/inlets_outlets.json
new file mode 100644
index 00000000..2b53da73
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/inlets_outlets.json
@@ -0,0 +1,28 @@
+{
+    "Geometry": {
+            "OverallDomain": {
+                    "x" : {"nblocks": 10, "size_per_block": 1.0},
+                    "y" : {"nblocks": 11, "size_per_block": 1.0},
+                    "z" : {"nblocks": 5, "size_per_block": 1.0}
+            },
+            "Fluids": [
+                    [ [0,0,0], [9,0,0] ],
+                    [ [9,0,0], [9,0,4] ],
+                    [ [9,0,4], [0,0,4] ],
+                    [ [0,1,4], [0,4,4] ],
+                    [ [0,4,4], [0,10,4] ],
+                    [ [0,4,4], [0,4,0] ],
+                    [ [0,4,0], [0,10,0] ],
+                    [ [0,4,0], [0,1,0] ]
+            ]
+    },
+    "inlets": [
+        {"branch_id": 0, "type": "circle", "frac_space": 0.2222222222222222, "normal_dir": 1, "radius": 0.4, "nelements": 50, "block_pos": "bottom"},
+        {"branch_id": 0, "type": "circle", "frac_space": 0.5, "radius": 0.4, "normal_dir": 1,"nelements": 50, "block_pos": "bottom"},
+        {"branch_id": 0, "type": "circle", "frac_space": 0.7777777777777778, "radius": 0.4, "normal_dir": 1,"nelements": 50, "block_pos": "bottom"}
+    ],
+    "outlets": [
+        {"branch_id": 6, "type": "circle", "frac_space": 1, "normal_dir": 1, "radius": 0.4, "nelements": 50, "block_pos": "top"},
+        {"branch_id": 4, "type": "circle", "frac_space": 1, "normal_dir": 1, "radius": 0.4, "nelements": 50, "block_pos": "top"}
+    ]
+}
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/mesh.json b/papers/scaleup/generate_scaleup_runs/template/system/mesh.json
new file mode 100644
index 00000000..29841d7e
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/mesh.json
@@ -0,0 +1,26 @@
+{
+        "Meshing": {
+                "Blockwise": {
+                        "x" : 10,
+                        "y" : 10,
+                        "z" : 10
+                }
+        },
+        "Geometry": {
+                "OverallDomain": {
+                        "x" : {"nblocks": 10, "size_per_block": 1.0},
+                        "y" : {"nblocks": 11, "size_per_block": 1.0},
+                        "z" : {"nblocks": 5, "size_per_block": 1.0}
+                },
+                "Fluids": [
+			[ [0,0,0], [9,0,0] ],
+                        [ [9,0,0], [9,0,4] ],
+                        [ [9,0,4], [0,0,4] ],
+                        [ [0,1,4], [0,4,4] ],
+                        [ [0,4,4], [0,10,4] ],
+                        [ [0,4,4], [0,4,0] ],
+                        [ [0,4,0], [0,10,0] ],
+                        [ [0,4,0], [0,1,0] ]
+                ]
+        }
+}
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/mixers.json b/papers/scaleup/generate_scaleup_runs/template/system/mixers.json
new file mode 100644
index 00000000..b6224fb7
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/mixers.json
@@ -0,0 +1,29 @@
+{
+    "Meshing": {
+                "Blockwise": {
+                        "x" : 10,
+                        "y" : 10,
+                        "z" : 10
+                }
+        },
+    "Geometry": {
+            "OverallDomain": {
+                    "x" : {"nblocks": 10, "size_per_block": 1.0, "rescale": 2.7615275385627096},
+                    "y" : {"nblocks": 11, "size_per_block": 1.0, "rescale": 2.7615275385627096},
+                    "z" : {"nblocks": 5, "size_per_block": 1.0, "rescale": 2.7615275385627096}
+            },
+            "Fluids": [
+		    [ [0,0,0], [9,0,0] ],
+                    [ [9,0,0], [9,0,4] ],
+                    [ [9,0,4], [0,0,4] ],
+                    [ [0,1,4], [0,4,4] ],
+                    [ [0,4,4], [0,10,4] ],
+                    [ [0,4,4], [0,4,0] ],
+                    [ [0,4,0], [0,10,0] ],
+                    [ [0,4,0], [0,1,0] ]
+            ]
+    },
+    "mixers": [ 
+        {"branch_id": 2, "frac_space": 0.5, "start_time": 4, "power": 1500,  "sign": "+"}
+    ]                   
+} 
diff --git a/papers/scaleup/generate_scaleup_runs/template/system/setFieldsDict b/papers/scaleup/generate_scaleup_runs/template/system/setFieldsDict
new file mode 100644
index 00000000..89a797b9
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/system/setFieldsDict
@@ -0,0 +1,37 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     | Website:  https://openfoam.org
+    \\  /    A nd           | Version:  dev
+     \\/     M anipulation  |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      setFieldsDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+defaultFieldValues
+(
+    volScalarFieldValue alpha.gas 0.99
+    volScalarFieldValue alpha.liquid 0.01
+);
+
+regions
+(
+    boxToCell
+    {
+        box (-1.0 -1.0 -1.0) (552.3 11.046 552.3);
+        fieldValues
+        (
+            volScalarFieldValue alpha.gas 0.01
+            volScalarFieldValue alpha.liquid 0.99
+        );
+    }
+);
+
+
+// ************************************************************************* //
diff --git a/papers/scaleup/generate_scaleup_runs/template/test.foam b/papers/scaleup/generate_scaleup_runs/template/test.foam
new file mode 100644
index 00000000..e69de29b
diff --git a/papers/scaleup/generate_scaleup_runs/template/writeGlobalVars.py b/papers/scaleup/generate_scaleup_runs/template/writeGlobalVars.py
new file mode 100644
index 00000000..e64d69e3
--- /dev/null
+++ b/papers/scaleup/generate_scaleup_runs/template/writeGlobalVars.py
@@ -0,0 +1,42 @@
+import os
+
+import numpy as np
+
+from bird.utilities.ofio import *
+
+
+def writeGvars(inletA, liqVol):
+    filename_tmp = os.path.join("constant", "globalVars_temp")
+    with open(filename_tmp, "r+") as f:
+        lines = f.readlines()
+    filename = os.path.join("constant", "globalVars")
+    with open(filename, "w+") as f:
+        for line in lines:
+            if line.startswith("inletA"):
+                f.write(f"inletA\t{inletA:g};\n")
+            elif line.startswith("liqVol"):
+                f.write(f"liqVol\t{liqVol:g};\n")
+            else:
+                f.write(line)
+
+
+def readInletArea():
+    filename = os.path.join(
+        "postProcessing",
+        "patchIntegrate(patch=inlet,field=alpha.gas)",
+        "0",
+        "surfaceFieldValue.dat",
+    )
+    return read_surface_field_value(filename)
+
+
+def getLiqVol():
+    volume_field, _ = read_cell_volumes(".")
+    alpha_field, _ = read_field(".", "0", field_name="alpha.liquid")
+    return np.sum(volume_field * alpha_field)
+
+
+if __name__ == "__main__":
+    A = readInletArea()
+    V = getLiqVol()
+    writeGvars(A, V)
diff --git a/tests/io/test_read_foam_dict.py b/tests/io/test_read_foam_dict.py
index e8692b92..16451d52 100644
--- a/tests/io/test_read_foam_dict.py
+++ b/tests/io/test_read_foam_dict.py
@@ -1,9 +1,36 @@
 import os
+import tempfile
 from pathlib import Path
 
 import numpy as np
 
-from bird.utilities.ofio import read_openfoam_dict
+from bird.utilities.ofio import read_gravity, read_openfoam_dict
+
+
+def test_read_gravity():
+    """
+    Test reading gravity magnitude from `constant/g`, with a 9.81 fallback
+    """
+    case_folder = os.path.join(
+        Path(__file__).parent,
+        " .. ".strip(),
+        " .. ".strip(),
+        "tutorial_cases",
+        "OF9",
+        "loop_reactor_mixing_swirl",
+    )
+    assert read_gravity(case_folder) == 9.81
+
+    # custom vertical gravity
+    with tempfile.TemporaryDirectory() as tmp:
+        os.makedirs(os.path.join(tmp, "constant"))
+        with open(os.path.join(tmp, "constant", "g"), "w") as f:
+            f.write("dimensions [0 1 -2 0 0 0 0];\nvalue (0 -3.0 0);\n")
+        assert read_gravity(tmp) == 3.0
+
+    # missing constant/g -> 9.81 fallback
+    with tempfile.TemporaryDirectory() as tmp:
+        assert read_gravity(tmp) == 9.81
 
 
 def test_read_phaseProperties():
diff --git a/tests/io/test_read_global_vars.py b/tests/io/test_read_global_vars.py
index 8fb689d2..85adba8e 100644
--- a/tests/io/test_read_global_vars.py
+++ b/tests/io/test_read_global_vars.py
@@ -3,7 +3,23 @@
 
 import numpy as np
 
-from bird.utilities.ofio import read_global_vars
+from bird.utilities.ofio import read_global_vars, read_surface_tension
+
+
+def test_read_surface_tension():
+    """
+    Test backing surface tension out of `constant/phaseProperties`
+    """
+    case_folder = os.path.join(
+        Path(__file__).parent,
+        " .. ".strip(),
+        " .. ".strip(),
+        "tutorial_cases",
+        "OF9",
+        "loop_reactor_mixing_swirl",
+    )
+    # sigma is `$sigmaLiq` in phaseProperties, resolved via globalVars
+    assert read_surface_tension(case_folder) == 0.07
 
 
 def test_read_global_vars():
diff --git a/tests/postprocess/test_dimensionless.py b/tests/postprocess/test_dimensionless.py
new file mode 100644
index 00000000..68a35784
--- /dev/null
+++ b/tests/postprocess/test_dimensionless.py
@@ -0,0 +1,130 @@
+import os
+import tempfile
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+from bird.postprocess.post_quantities import (
+    compute_froude_number,
+    compute_instantaneous_kl,
+    compute_sherwood_number,
+    compute_weber_number,
+    froude,
+    sherwood,
+    weber,
+)
+from bird.utilities.ofio import read_global_vars
+
+
+def write_gravity_case(root, gy):
+    """Write a minimal constant/g with vertical gravity gy."""
+    os.makedirs(os.path.join(root, "constant"), exist_ok=True)
+    with open(os.path.join(root, "constant", "g"), "w") as f:
+        f.write("FoamFile\n{\n    class uniformDimensionedVectorField;\n}\n")
+        f.write("dimensions      [0 1 -2 0 0 0 0];\n")
+        f.write(f"value           (0 {gy} 0);\n")
+
+
+def write_dimensionless_case(root, u_x, rho, sigma, cell_volumes):
+    """Case with uniform U.liquid=(u_x,0,0), rho, all-liquid, and sigma."""
+    os.makedirs(os.path.join(root, "0"), exist_ok=True)
+    os.makedirs(os.path.join(root, "constant"), exist_ok=True)
+
+    def write_field(name, foam_class, body):
+        with open(os.path.join(root, "0", name), "w") as f:
+            f.write("FoamFile\n{\n    format      ascii;\n")
+            f.write(f"    class       {foam_class};\n")
+            f.write(f"    object      {name};\n}}\n\n")
+            f.write("dimensions      [0 0 0 0 0 0 0];\n\n")
+            f.write(body)
+
+    entries = "\n".join(f"{v:.10g}" for v in cell_volumes)
+    write_field(
+        "V",
+        "volScalarField",
+        "internalField   nonuniform List<scalar> \n"
+        f"{len(cell_volumes)}\n(\n{entries}\n)\n;\n",
+    )
+    write_field(
+        "alpha.liquid", "volScalarField", "internalField   uniform 1;\n"
+    )
+    write_field(
+        "U.liquid",
+        "volVectorField",
+        f"internalField   uniform ({u_x} 0 0);\n",
+    )
+    write_field(
+        "thermo:rho.liquid",
+        "volScalarField",
+        f"internalField   uniform {rho};\n",
+    )
+    with open(os.path.join(root, "constant", "phaseProperties"), "w") as f:
+        f.write("surfaceTension\n(\n    (gas and liquid)\n    {\n")
+        f.write(
+            f"        type            constant;\n        sigma  {sigma};\n"
+        )
+        f.write("    }\n);\n")
+
+
+def test_froude():
+    # default gravity 9.81
+    assert froude(1.0, 1.0) == pytest.approx(1.0 / np.sqrt(9.81))
+    # Fr = U / sqrt(g*L); 2 / sqrt(16*0.25) = 1
+    assert froude(2.0, 0.25, gravity=16.0) == pytest.approx(1.0)
+
+
+def test_weber():
+    # We = rho*U^2*L/sigma; 1000 * 4 * 0.5 / 100 = 20
+    assert weber(1000.0, 2.0, 0.5, 100.0) == pytest.approx(20.0)
+
+
+def test_sherwood():
+    # Sh = kL*L/D; 1e-4 * 0.5 / 1e-5 = 5
+    assert sherwood(1e-4, 0.5, 1e-5) == pytest.approx(5.0)
+
+
+def test_compute_froude_number():
+    # velocity = |U.liquid| = 3, g = 9 -> Fr = 3 / sqrt(9*0.25) = 2
+    with tempfile.TemporaryDirectory() as tmp:
+        write_dimensionless_case(
+            tmp, u_x=3.0, rho=1000.0, sigma=0.05, cell_volumes=[1.0, 2.0, 3.0]
+        )
+        write_gravity_case(tmp, -9.0)
+        fr, _ = compute_froude_number(tmp, "0", length=0.25, volume_time="0")
+    assert fr == pytest.approx(2.0)
+
+
+def test_compute_weber_number():
+    # We = rho*U^2*L/sigma = 1000 * 9 * 0.2 / 0.05 = 36000
+    with tempfile.TemporaryDirectory() as tmp:
+        write_dimensionless_case(
+            tmp, u_x=3.0, rho=1000.0, sigma=0.05, cell_volumes=[1.0, 2.0, 3.0]
+        )
+        we, _ = compute_weber_number(tmp, "0", length=0.2, volume_time="0")
+    assert we == pytest.approx(1000.0 * 9.0 * 0.2 / 0.05)
+
+
+def test_compute_sherwood_number():
+    case_folder = os.path.join(
+        Path(__file__).parent,
+        " .. ".strip(),
+        " .. ".strip(),
+        "bird",
+        "postprocess",
+        "data_conditional_mean",
+    )
+    # Sh = kL * L / D_molecular, with kL from compute_instantaneous_kl and
+    # D_CO2 read from globalVars. kL is in m/h and D in m2/s, so kL is
+    # converted to m/s (/3600) for Sh to be dimensionless.
+    kl_spec, _, _ = compute_instantaneous_kl(
+        species_names="CO2",
+        case_folder=case_folder,
+        time_folder="80",
+        volume_time="1",
+    )
+    diffusivity = float(read_global_vars(case_folder)["D_CO2"])
+    sh, _ = compute_sherwood_number(
+        case_folder, "80", length=0.1, species_name="CO2", volume_time="1"
+    )
+    assert sh == pytest.approx((kl_spec["CO2"] / 3600) * 0.1 / diffusivity)
diff --git a/tests/postprocess/test_loop_velocity.py b/tests/postprocess/test_loop_velocity.py
new file mode 100644
index 00000000..7b891b82
--- /dev/null
+++ b/tests/postprocess/test_loop_velocity.py
@@ -0,0 +1,205 @@
+import json
+import os
+import tempfile
+from pathlib import Path
+
+import numpy as np
+
+from bird.postprocess.post_quantities import (
+    build_loop_direction_field,
+    build_loop_direction_field_from_path,
+    compute_loop_velocity,
+    propose_loop_boxes_block_rect,
+)
+
+
+def write_min_case(root, u_vectors, cell_volumes, alpha_gas=None):
+    """Minimal case with a vector U.liquid, scalar V and optional alpha.gas."""
+    os.makedirs(os.path.join(root, "0"), exist_ok=True)
+
+    def write_field(name, foam_class, body):
+        with open(os.path.join(root, "0", name), "w") as f:
+            f.write("FoamFile\n{\n    format      ascii;\n")
+            f.write(f"    class       {foam_class};\n")
+            f.write(f"    object      {name};\n}}\n\n")
+            f.write("dimensions      [0 0 0 0 0 0 0];\n\n")
+            f.write(body)
+
+    def scalar(values):
+        entries = "\n".join(f"{v:.10g}" for v in values)
+        return (
+            "internalField   nonuniform List<scalar> \n"
+            f"{len(values)}\n(\n{entries}\n)\n;\n"
+        )
+
+    def vector(vectors):
+        entries = "\n".join(
+            f"({x:.10g} {y:.10g} {z:.10g})" for x, y, z in vectors
+        )
+        return (
+            "internalField   nonuniform List<vector> \n"
+            f"{len(vectors)}\n(\n{entries}\n)\n;\n"
+        )
+
+    write_field("V", "volScalarField", scalar(cell_volumes))
+    write_field("U.liquid", "volVectorField", vector(u_vectors))
+    if alpha_gas is not None:
+        write_field("alpha.gas", "volScalarField", scalar(alpha_gas))
+
+
+def test_build_loop_direction_field():
+    # Four cells: two in box A (+x), one in box B (+y), one in no box
+    cell_centers = np.array(
+        [[0.5, 0.0, 0.0], [1.5, 0.0, 0.0], [5.0, 5.0, 0.0], [9.0, 9.0, 9.0]]
+    )
+    boxes = [
+        {"min": [0, -1, -1], "max": [2, 1, 1], "direction": [3, 0, 0]},
+        {"min": [4, 4, -1], "max": [6, 6, 1], "direction": [0, 2, 0]},
+    ]
+    field = build_loop_direction_field(cell_centers, boxes)
+
+    assert field.shape == (4, 3)
+    # direction is normalized to a unit vector
+    np.testing.assert_allclose(field[0], [1, 0, 0])
+    np.testing.assert_allclose(field[1], [1, 0, 0])
+    np.testing.assert_allclose(field[2], [0, 1, 0])
+    # uncovered cell stays NaN
+    assert np.all(np.isnan(field[3]))
+
+    # a cell inside two boxes is ambiguous -> error
+    overlap = [
+        {"min": [0, -1, -1], "max": [2, 1, 1], "direction": [1, 0, 0]},
+        {"min": [1, -1, -1], "max": [3, 1, 1], "direction": [0, 1, 0]},
+    ]
+    try:
+        build_loop_direction_field(cell_centers, overlap)
+        raised = False
+    except ValueError:
+        raised = True
+    assert raised
+
+    # boxes that match no cell (e.g. wrong coordinate frame / rescale) -> error
+    far = [
+        {
+            "min": [100, 100, 100],
+            "max": [101, 101, 101],
+            "direction": [1, 0, 0],
+        }
+    ]
+    try:
+        build_loop_direction_field(cell_centers, far)
+        raised_empty = False
+    except ValueError:
+        raised_empty = True
+    assert raised_empty
+
+
+def test_build_loop_direction_field_from_path():
+    # Path: (0,0,0)->(1,0,0) [+x] then (1,0,0)->(1,1,0) [+y]
+    path = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0]])
+    cell_centers = np.array(
+        [
+            [0.5, 0.05, 0.0],  # near the +x segment
+            [1.0, 0.5, 0.0],  # on the +y segment
+            [0.5, 5.0, 0.0],  # far from the path
+        ]
+    )
+    field = build_loop_direction_field_from_path(
+        cell_centers, path, max_dist=0.5
+    )
+
+    np.testing.assert_allclose(field[0], [1, 0, 0], atol=1e-12)
+    np.testing.assert_allclose(field[1], [0, 1, 0], atol=1e-12)
+    assert np.all(np.isnan(field[2]))
+
+    # every cell beyond max_dist (wrong frame) -> error
+    try:
+        build_loop_direction_field_from_path(
+            np.array([[50.0, 50.0, 50.0]]), path, max_dist=0.5
+        )
+        raised = False
+    except ValueError:
+        raised = True
+    assert raised
+
+
+def test_propose_loop_boxes_block_rect():
+    template = os.path.join(
+        Path(__file__).parent,
+        " .. ".strip(),
+        " .. ".strip(),
+        "bird",
+        "meshing",
+        "block_rect_mesh_templates",
+        "loopReactor",
+        "input.json",
+    )
+    geometry = json.load(open(template))["Geometry"]
+    # rescale=None -> base units (factor 1.0)
+    boxes = propose_loop_boxes_block_rect(geometry, rescale=None)
+
+    # two Fluids branches of 4 blocks -> 3 segments each -> 6 legs
+    assert len(boxes) == 6
+
+    # first leg: [0,0,0]->[9,0,0], centres at 0.5..9.5, trimmed half a block
+    first = boxes[0]
+    np.testing.assert_allclose(first["direction"], [1, 0, 0])
+    np.testing.assert_allclose(first["min"], [1.0, 0.0, 0.0])
+    np.testing.assert_allclose(first["max"], [9.0, 1.0, 1.0])
+
+    # a float rescale scales the box coordinates but not the direction
+    scaled = propose_loop_boxes_block_rect(geometry, rescale=2.0)
+    np.testing.assert_allclose(scaled[0]["min"], [2.0, 0.0, 0.0])
+    np.testing.assert_allclose(scaled[0]["max"], [18.0, 2.0, 2.0])
+    np.testing.assert_allclose(scaled[0]["direction"], [1, 0, 0])
+
+
+def test_compute_loop_velocity():
+    # Two cells pointing along +x, direction +x -> loop velocity = weighted |Ux|
+    u_vectors = [[2.0, 0.0, 0.0], [4.0, 0.0, 0.0]]
+    cell_volumes = [1.0, 3.0]
+    direction_field = np.array([[1.0, 0.0, 0.0], [1.0, 0.0, 0.0]])
+
+    # all-liquid (alpha.gas = 0) -> volume-weighted mean = (2*1 + 4*3)/(1+3) = 3.5
+    with tempfile.TemporaryDirectory() as tmp:
+        write_min_case(tmp, u_vectors, cell_volumes, alpha_gas=[0.0, 0.0])
+        v, _ = compute_loop_velocity(
+            tmp, "0", direction_field, volume_time="0"
+        )
+    assert abs(v - 3.5) < 1e-10
+
+    # a NaN direction excludes its cell: only the first cell counts -> 2.0
+    with tempfile.TemporaryDirectory() as tmp:
+        write_min_case(tmp, u_vectors, cell_volumes, alpha_gas=[0.0, 0.0])
+        partial = np.array([[1.0, 0.0, 0.0], [np.nan, np.nan, np.nan]])
+        v_partial, _ = compute_loop_velocity(
+            tmp, "0", partial, volume_time="0"
+        )
+    assert abs(v_partial - 2.0) < 1e-10
+
+    # reversed direction flips the sign
+    with tempfile.TemporaryDirectory() as tmp:
+        write_min_case(tmp, u_vectors, cell_volumes, alpha_gas=[0.0, 0.0])
+        reversed_dir = np.array([[-1.0, 0.0, 0.0], [-1.0, 0.0, 0.0]])
+        v_rev, _ = compute_loop_velocity(
+            tmp, "0", reversed_dir, volume_time="0"
+        )
+    assert abs(v_rev + 3.5) < 1e-10
+
+    # liquid weighting from alpha.gas: weights = vol*(1-alpha_gas) = [1, 1.5]
+    with tempfile.TemporaryDirectory() as tmp:
+        write_min_case(tmp, u_vectors, cell_volumes, alpha_gas=[0.0, 0.5])
+        v_alpha, _ = compute_loop_velocity(
+            tmp, "0", direction_field, volume_time="0"
+        )
+    assert abs(v_alpha - (2 * 1.0 + 4 * 1.5) / 2.5) < 1e-10
+
+    # neither alpha.gas nor alpha.liquid present -> error
+    with tempfile.TemporaryDirectory() as tmp:
+        write_min_case(tmp, u_vectors, cell_volumes)
+        try:
+            compute_loop_velocity(tmp, "0", direction_field, volume_time="0")
+            raised = False
+        except FileNotFoundError:
+            raised = True
+    assert raised
diff --git a/tests/postprocess/test_post_quantities.py b/tests/postprocess/test_post_quantities.py
index 5dbafca8..65ab255f 100644
--- a/tests/postprocess/test_post_quantities.py
+++ b/tests/postprocess/test_post_quantities.py
@@ -12,11 +12,16 @@
     _get_ind_liq,
     compute_ave_bubble_diam,
     compute_ave_conc_liq,
+    compute_ave_liquid_density,
+    compute_ave_liquid_velocity,
     compute_ave_y_liq,
+    compute_fitted_kl,
     compute_fitted_kla,
     compute_gas_holdup,
+    compute_instantaneous_kl,
     compute_instantaneous_kla,
     compute_superficial_gas_velocity,
+    interfacial_area,
 )
 
 
@@ -55,8 +60,8 @@ def test_compute_gh():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -106,8 +111,8 @@ def test_compute_diam():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -143,8 +148,8 @@ def test_compute_superficial_gas_velocity():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean/",
@@ -201,8 +206,8 @@ def test__superficial_velocity_pv():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean/",
@@ -232,8 +237,8 @@ def test_ave_y_liq():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -300,8 +305,8 @@ def test_ave_conc_liq():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -354,8 +359,8 @@ def test_instantaneous_kla():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -422,8 +427,8 @@ def test_fitted_kla():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -475,8 +480,8 @@ def test_get_ind_gas():
     """
     case_folder = os.path.join(
         Path(__file__).parent,
-        "..",
-        "..",
+        " .. ".strip(),
+        " .. ".strip(),
         "bird",
         "postprocess",
         "data_conditional_mean",
@@ -518,3 +523,131 @@ def test_get_ind_gas():
     # A uniform liquid field needs no filtering at all, rather than selecting
     # a single cell
     assert ind_liq_unif is None
+
+
+def _write_liquid_fields(root, u_vector, rho, cell_volumes):
+    """Minimal case: all-liquid, uniform U.liquid and rho, nonuniform V."""
+    os.makedirs(os.path.join(root, "0"), exist_ok=True)
+
+    def write_field(name, foam_class, body):
+        with open(os.path.join(root, "0", name), "w") as f:
+            f.write("FoamFile\n{\n    format      ascii;\n")
+            f.write(f"    class       {foam_class};\n")
+            f.write(f"    object      {name};\n}}\n\n")
+            f.write("dimensions      [0 0 0 0 0 0 0];\n\n")
+            f.write(body)
+
+    entries = "\n".join(f"{v:.10g}" for v in cell_volumes)
+    write_field(
+        "V",
+        "volScalarField",
+        "internalField   nonuniform List<scalar> \n"
+        f"{len(cell_volumes)}\n(\n{entries}\n)\n;\n",
+    )
+    write_field(
+        "alpha.liquid", "volScalarField", "internalField   uniform 1;\n"
+    )
+    write_field(
+        "U.liquid",
+        "volVectorField",
+        f"internalField   uniform ({u_vector[0]} {u_vector[1]} "
+        f"{u_vector[2]});\n",
+    )
+    write_field(
+        "thermo:rho.liquid",
+        "volScalarField",
+        f"internalField   uniform {rho};\n",
+    )
+
+
+def test_compute_ave_liquid_density():
+    with tempfile.TemporaryDirectory() as tmp:
+        _write_liquid_fields(tmp, (1.0, 0.0, 0.0), 1050.0, [1.0, 2.0, 3.0])
+        rho, _ = compute_ave_liquid_density(tmp, "0", volume_time="0")
+    assert rho == pytest.approx(1050.0)
+
+
+def test_compute_ave_liquid_velocity():
+    # |U.liquid| = |(3,4,0)| = 5
+    with tempfile.TemporaryDirectory() as tmp:
+        _write_liquid_fields(tmp, (3.0, 4.0, 0.0), 1000.0, [1.0, 2.0, 3.0])
+        velocity, _ = compute_ave_liquid_velocity(tmp, "0", volume_time="0")
+    assert velocity == pytest.approx(5.0)
+
+
+def test_interfacial_area():
+    """
+    Test the interfacial area a = 6 * holdup / diameter
+    """
+    assert interfacial_area(0.2, 0.005) == pytest.approx(240.0)
+
+
+def test_instantaneous_kl():
+    """
+    Test for instantaneous kl calculation (volume-averaged Higbie coefficient)
+    """
+    case_folder = os.path.join(
+        Path(__file__).parent,
+        " .. ".strip(),
+        " .. ".strip(),
+        "bird",
+        "postprocess",
+        "data_conditional_mean",
+    )
+    kl_list, cstar_list, _ = compute_instantaneous_kl(
+        species_names=["CO2"],
+        case_folder=case_folder,
+        time_folder="79",
+        volume_time="1",
+    )
+    kl_str, _, _ = compute_instantaneous_kl(
+        species_names="CO2",
+        case_folder=case_folder,
+        time_folder="79",
+        volume_time="1",
+    )
+    # positive, finite, and the single/list species forms agree
+    assert kl_list["CO2"] > 0 and np.isfinite(kl_list["CO2"])
+    assert kl_str["CO2"] == pytest.approx(kl_list["CO2"])
+
+    kla_spec, cstar_kla, _ = compute_instantaneous_kla(
+        species_names=["CO2"],
+        case_folder=case_folder,
+        time_folder="79",
+        volume_time="1",
+    )
+    # cstar is shared with compute_instantaneous_kla
+    assert cstar_list["CO2"] == pytest.approx(cstar_kla["CO2"])
+    # kL (= <coef>) and kLa (= <coef * a>) are distinct quantities
+    assert kl_list["CO2"] != pytest.approx(kla_spec["CO2"])
+
+
+def test_fitted_kl():
+    """
+    Test for fitted kl calculation (fitted kLa / interfacial area)
+    """
+    case_folder = os.path.join(
+        Path(__file__).parent,
+        " .. ".strip(),
+        " .. ".strip(),
+        "bird",
+        "postprocess",
+        "data_conditional_mean",
+    )
+    # dummy time folders so the fit has enough snapshots
+    for time_folder in [str(entry) for entry in range(81, 89)]:
+        shutil.copytree(
+            os.path.join(case_folder, "80"),
+            os.path.join(case_folder, time_folder),
+        )
+    kl_spec, _, _ = compute_fitted_kl(
+        species_names=["CO2"],
+        case_folder=case_folder,
+        num_warmup=100,
+        num_samples=100,
+    )
+    for time_folder in [str(entry) for entry in range(81, 89)]:
+        shutil.rmtree(os.path.join(case_folder, time_folder))
+
+    assert "mean" in kl_spec["CO2"] and "std" in kl_spec["CO2"]
+    assert np.isfinite(kl_spec["CO2"]["mean"])
diff --git a/tests/postprocess/test_stats.py b/tests/postprocess/test_stats.py
index 60f7a69f..5f1ff631 100644
--- a/tests/postprocess/test_stats.py
+++ b/tests/postprocess/test_stats.py
@@ -4,7 +4,7 @@
 import pytest
 
 from bird import logger
-from bird.postprocess.stats import calc_mean
+from bird.postprocess.stats import calc_mean, steady_stat
 
 
 def test_mean_stats_uniform():
@@ -59,3 +59,34 @@ def test_mean_stats_nonuniform():
 
     # Make sure non uniform signal is correctly treated
     assert abs(unc_non_unif - unc_unif) / unc_unif < 0.1
+
+
+def test_steady_stat():
+    """
+    Test the windowed (mean, 1-sigma) steady-state statistic
+    """
+    t = np.linspace(0, 10, 1000)
+    signal = np.cos(t * 2 * np.pi)
+
+    # explicit window: stat is calc_mean over the last 2 s, 95% -> 1-sigma
+    mask = t >= t.max() - 2.0
+    mean_ref, unc95_ref = calc_mean(signal[mask], t[mask])
+    mean_val, sigma = steady_stat(signal, t, window=2.0)
+    assert mean_val == pytest.approx(mean_ref)
+    assert sigma == pytest.approx(unc95_ref / 1.96)
+
+    # default window = 10% of the span (last 1 s here)
+    default_mask = t >= t.max() - 0.1 * (t.max() - t.min())
+    mean_def_ref, _ = calc_mean(signal[default_mask], t[default_mask])
+    mean_def, _ = steady_stat(signal, t)
+    assert mean_def == pytest.approx(mean_def_ref)
+
+    # empty and all-nan series -> (nan, nan)
+    mean_empty, sigma_empty = steady_stat([], [])
+    assert np.isnan(mean_empty) and np.isnan(sigma_empty)
+    mean_nan, sigma_nan = steady_stat([np.nan, np.nan], [0.0, 1.0])
+    assert np.isnan(mean_nan) and np.isnan(sigma_nan)
+
+    # a single sample in the window -> (value, 0.0)
+    mean_one, sigma_one = steady_stat([1.0, 3.5], [0.0, 1.0], window=0.5)
+    assert mean_one == 3.5 and sigma_one == 0.0
diff --git a/tests/postprocess/test_transport.py b/tests/postprocess/test_transport.py
new file mode 100644
index 00000000..44f2fa01
--- /dev/null
+++ b/tests/postprocess/test_transport.py
@@ -0,0 +1,52 @@
+import os
+import tempfile
+
+from bird.postprocess.post_quantities import compute_turbulent_diffusivity
+
+
+def write_scalar_case(root, fields):
+    """Write each {name: values} as a nonuniform scalar field in the 0 folder."""
+    os.makedirs(os.path.join(root, "0"), exist_ok=True)
+    for name, values in fields.items():
+        entries = "\n".join(f"{v:.10g}" for v in values)
+        with open(os.path.join(root, "0", name), "w") as f:
+            f.write("FoamFile\n{\n    format      ascii;\n")
+            f.write("    class       volScalarField;\n")
+            f.write(f"    object      {name};\n}}\n\n")
+            f.write("dimensions      [0 0 0 0 0 0 0];\n\n")
+            f.write(
+                "internalField   nonuniform List<scalar> \n"
+                f"{len(values)}\n(\n{entries}\n)\n;\n"
+            )
+
+
+def test_compute_turbulent_diffusivity():
+    # alpha.liquid selects cells 0,1 (cell 2 is gas). D = alphat/rho = [1,2,3];
+    # volume-weighted over the liquid = (1*1 + 2*1)/(1+1) = 1.5
+    with tempfile.TemporaryDirectory() as tmp:
+        write_scalar_case(
+            tmp,
+            {
+                "alpha.liquid": [1.0, 1.0, 0.0],
+                "alphat.liquid": [2.0, 4.0, 6.0],
+                "rho.liquid": [2.0, 2.0, 2.0],
+                "V": [1.0, 1.0, 1.0],
+            },
+        )
+        d_turb, _ = compute_turbulent_diffusivity(tmp, "0")
+    assert abs(d_turb - 1.5) < 1e-10
+
+    # no alphat.liquid -> nut.liquid / Prt (0.85). nut = [0.85, 1.70] -> [1, 2]
+    with tempfile.TemporaryDirectory() as tmp:
+        write_scalar_case(
+            tmp,
+            {
+                "alpha.liquid": [1.0, 1.0],
+                "nut.liquid": [0.85, 1.70],
+                "rho.liquid": [1.0, 1.0],
+                "V": [1.0, 3.0],
+            },
+        )
+        d_fallback, _ = compute_turbulent_diffusivity(tmp, "0")
+    # volume-weighted (1*1 + 2*3)/(1+3) = 1.75
+    assert abs(d_fallback - 1.75) < 1e-10