bdm.core.toml

[visualization]
export = true
interval = 200

# Keratinocyte agent viz registered dynamically (wound_enabled only)

[[visualize_diffusion]]
  name = "Stratum"

[[visualize_diffusion]]
  name = "Vascular"

# ---- Visualization coloring ----
# Named colormaps applied to ParaView state file by scripts/viz/patch_pvsm.py.
# First colormap section is the default; others match by name substring.
# Each cN = [value, R, G, B] entry defines one color stop.

[visualization.colormap.skin_strata]
color_space = "Step"
c0 = [0.0, 0.831, 0.400, 0.392]   # Basale
c1 = [1.0, 0.910, 0.590, 0.478]   # Spinosum
c2 = [2.0, 0.941, 0.788, 0.529]   # Granulosum
c3 = [3.0, 0.961, 0.902, 0.827]   # Corneum
c4 = [4.0, 0.710, 0.325, 0.294]   # Dermis
c5 = [5.0, 0.750, 0.480, 0.470]   # Scar Basale
c6 = [6.0, 0.820, 0.620, 0.550]   # Scar Spinosum
c7 = [7.0, 0.870, 0.750, 0.620]   # Scar Granulosum
c8 = [8.0, 0.900, 0.850, 0.780]   # Scar Corneum
c9 = [10.0, 0.929, 0.780, 0.686]  # Papillary dermis (light peach)
c10 = [11.0, 0.729, 0.506, 0.400] # Reticular dermis (warm brown)
c11 = [12.0, 0.529, 0.353, 0.294] # Hypodermis (deep brown)

[visualization.colormap.immune_types]
color_space = "Step"
c0 = [0.0, 1.000, 1.000, 1.000]   # Neutrophil (white)
c1 = [1.0, 1.000, 0.850, 0.200]   # Macrophage (yellow)

[visualization.colormap.tumor_types]
color_space = "Step"
c0 = [0.0, 0.200, 0.800, 0.200]   # Tumor

[visualization.glyph]
theta_resolution = 8
phi_resolution = 8

[visualization.rendering]
# Representation for diffusion grids: Volume, Surface, Outline, Slice
diffusion_representation = "Volume"

[visualization.opacity]
points = [[0.0, 0.04], [1.0, 0.35], [2.0, 0.4], [3.0, 0.45], [4.0, 0.55], [5.0, 0.65], [7.0, 0.75], [8.0, 0.8], [10.0, 0.85], [12.0, 0.9]]

[visualization.camera]
position = [-40.0, -80.0, 40.0]
focal_point = [15.0, 15.0, 15.0]
view_up = [0, 0, 1]
view_angle = 40

# ==================================================================
# Core tissue biology
# Module-specific params live in modules/*/config.toml and are merged
# at runtime by scripts/config/merge_config.py -> bdm.toml (gitignored).
# ==================================================================

[skin]
# ---- Dermis (continuum) ----
oxygen_diffusion = 0.1
oxygen_decay = 0.01
oxygen_basal_conc = 1.0
oxygen_decay_length = 8.0

# KGF growth factor
kgf_diffusion = 0
kgf_decay = 0
kgf_basal_conc = 2.0
kgf_half_maximal = 0.5
kgf_max_boost = 1.0
kgf_decay_length = 5.0

# Water / tissue moisture
water_diffusion = 1e-4
water_decay = 0.002
water_basal_conc = 1.0
water_decay_length = 12.0
water_recovery_rate = 0.02         # serum hydration rate per step (Sakai et al. 2005)
water_surface_loss_rate = 0.03
water_migration_threshold = 0.3
water_prolif_threshold = 0.4

# ---- Basale (agents on event) ----
g1_duration = 7.0
s_duration = 6.0
g2_duration = 3.0
m_duration = 1.0

growth_rate = 5
max_neighbors = 14
lateral_scatter = 0.3
max_ta_divisions = 4
division_diameter = 5.0
p_asymmetric = 0.7
stem_fraction = 0.50

repulsion_coeff = 5.0
attraction_coeff = 0.0

shedding_delay_h = 9999.9       # hours (disabled)
apoptosis_delay_h = 9999.9     # hours (disabled)

# ---- Epidermis (continuum) ----
calcium_diffusion = 0
calcium_decay = 0
calcium_basal = 0.05
calcium_peak = 1.5
calcium_midpoint_z = 18.0
calcium_steepness = 2.0

ca_spinous_threshold = 0.1
ca_granular_threshold = 0.5
ca_cornified_threshold = 1.0
spinous_threshold = 6.0

volume_z_spinous = 3.0
volume_z_granular = 18.0
volume_z_cornified = 25.0

# ---- Dermal sub-layers (z < 0) ----
dermal_z_papillary = -2.0
dermal_z_reticular = -8.0

# ---- Simulation ----
tissue_min = 0
tissue_max = 30
duration_days = 30

# ---- Dynamic field coupling ----
calcium_recovery_rate = 0.002
oxygen_prolif_threshold = 0.3
oxygen_recovery_enabled = true

# ---- Cell migration ----
migration_enabled = true
migration_speed = 2.0

# ---- Per-cell UWYN handoff ----
handoff_delay_h = 50            # hours before cell dissolves

# ---- Metrics export ----
metrics_interval_h = 10         # hours between CSV rows
metrics_autoopen = true

# ---- Performance: PDE sub-cycling ----
# Solve slow-diffusing fields every N steps instead of every step.
# Reduces FTCS solver invocations. 1 = every step (default), 5 = every 5.
# subcycle_slow: water (D=1e-4), hyaluronan (D=0.01), vascular (D=0.03)
# subcycle_medium: inflammation (D=0.05), TGF-beta (D=0.03), MMP, VEGF
subcycle_slow = 10
subcycle_medium = 5

# ---- Hot-reload ----
# Watch bdm.toml for changes and re-apply parameters at runtime.
# Edit bdm.toml while the sim runs to tune rates/thresholds interactively.
hot_reload = false

# ---- Derived composite fields ----
# Precomputed once per step from source grids. ECM quality, tissue viability,
# and wound microenvironment index for analysis and agent decisions.
[skin.derived]
ecm_weight_collagen = 0.4
ecm_weight_fibronectin = 0.3
ecm_weight_elastin = 0.2
ecm_weight_fibrin = 0.1
ecm_migration_boost = 1.5

# ---- Multi-resolution ----
# Structural fields (collagen, fibronectin, elastin, fibrin, scar, dermis,
# biofilm, hyaluronan, pH, tumor) at coarser grid for performance.
# 0 = same as grid_resolution. Nonzero = coarse resolution for structural fields.
grid_resolution_structural = 5

# ---- Debug profile ----
# Enable per-module diagnostic output (all default to false).
# Toggle in bdm.toml or pass --config to override.
[skin.debug]
immune = false         # immune cell writes, spawning, migration
fibroblast = false     # collagen, TGF-beta, state transitions
wound = false          # wound creation, resolution, coverage
scaled_grid = false    # ScaledGrid init (agent_factor)
perf = false           # wall-clock timing of major operations