From ae5c6c9dc97ef411f74458ccd5f5f91a56922166 Mon Sep 17 00:00:00 2001 From: michielstock Date: Mon, 10 Aug 2026 12:29:18 +0200 Subject: [PATCH 1/2] =?UTF-8?q?=F0=9F=8C=B1plantmodules?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Manifest.toml | 1931 +++++++++++++++++++++++++++++++++++++ dyad/PlantHydraulics.dyad | 246 +++++ viz_submission/_data.json | 1 + viz_submission/index.html | 996 +++++++++++++++++++ 4 files changed, 3174 insertions(+) create mode 100644 Manifest.toml create mode 100644 dyad/PlantHydraulics.dyad create mode 100644 viz_submission/_data.json create mode 100644 viz_submission/index.html diff --git a/Manifest.toml b/Manifest.toml new file mode 100644 index 0000000..41cc79d --- /dev/null +++ b/Manifest.toml @@ -0,0 +1,1931 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.12.6" +manifest_format = "2.0" +project_hash = "51acd021254e5ef8c3e280596e83dc2c6155ea22" + 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+version = "2022.3.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.7.0+0" diff --git a/dyad/PlantHydraulics.dyad b/dyad/PlantHydraulics.dyad new file mode 100644 index 0000000..aeabd50 --- /dev/null +++ b/dyad/PlantHydraulics.dyad @@ -0,0 +1,246 @@ +""" +Water potential connector. + +Acausal hydraulic connector for plant-water relations, following PlantModules.jl. +The potential variable is the total water potential Psi [MPa]; the flow variable +is the water flux F [g/h], taken positive when flowing *into* the component. +""" +connector HydraulicPort + "Total water potential [MPa]" + potential Psi::Real + "Water flux into the component [g h^-1]" + flow F::Real +end + +""" +Hydraulics-driven growing compartment (the core `hydraulic_module`). + +Models a cylindrical plant compartment whose volume grows with water accumulation +following the elastic-viscoplastic Lockhart model with a smooth (LogSumExp) yield +threshold. The total water potential combines turgor, osmotic (van 't Hoff) and +gravitational components. + +Growth per axis i: (1/l_i) d l_i/dt = phi (P - Gamma)_+ + (1/E) dP/dt +with the smooth threshold (x)_+ = LSE_alpha(x, 0) = (1/alpha) log(exp(alpha x) + 1). +""" +component HydraulicCompartment + "Water port" + port = HydraulicPort() + + "Cell-wall extensibility [MPa^-1 h^-1]" + parameter phi::Real = 0.02 + "Cell-wall elastic modulus [MPa]" + parameter E::Real = 50.0 + "Yield turgor pressure [MPa]" + parameter Gamma::Real = 0.3 + "Osmotically active metabolite content [mol cm^-3]" + parameter M::Real = 300e-6 + "Temperature [K]" + parameter T::Real = 298.15 + "Yield-threshold steepness" + parameter alpha::Real = 40.0 + "Height above ground [cm]" + parameter height::Real = 0.0 + "Water density [g cm^-3]" + parameter rho_w::Real = 1.0 + "Ideal gas constant [J mol^-1 K^-1]" + parameter R_gas::Real = 8.314 + "Gravitational-potential coefficient [MPa cm^-1] (= rho_w g)" + parameter c_grav::Real = 9.81e-5 + "Initial radius [cm]" + parameter Rd0::Real = 0.5 + "Initial length [cm]" + parameter L0::Real = 5.0 + "Initial turgor pressure [MPa]" + parameter P0::Real = 0.5 + + "Turgor (hydrostatic) pressure [MPa]" + variable P::Real + "Water content [g]" + variable W::Real + "Radius, growth axis 1 [cm]" + variable Rd::Real + "Length, growth axis 2 [cm]" + variable L::Real + "Volume [cm^3]" + variable V::Real + "Total water potential [MPa]" + variable Psi::Real + "Osmotic potential [MPa]" + variable Psi_osm::Real + "Smooth yield term [MPa]" + variable yield::Real +relations + initial Rd = Rd0 + initial L = L0 + initial P = P0 + + # Cylinder geometry and water content + V = π * Rd^2 * L + W = rho_w * V + + # Total water potential: turgor + osmotic (van 't Hoff) + gravitational + Psi_osm = -R_gas * T * M + Psi = P + Psi_osm + c_grav * height + + # Smooth yield threshold (LogSumExp) + yield = (1.0 / alpha) * log(exp(alpha * (P - Gamma)) + 1.0) + + # Water balance: net influx equals flow into the port + der(W) = port.F + + # Lockhart elastic-viscoplastic growth, one equation per axis + der(Rd) / Rd = phi * yield + der(P) / E + der(L) / L = phi * yield + der(P) / E + + # Expose the compartment's water potential at the port + port.Psi = Psi +end + +""" +Prescribed water-flux boundary. + +Draws a periodic water flux through its port. With default sign it removes water +from the connected compartment during the first half-period and returns it during +the second, giving a net-zero forcing suitable for exercising a compartment in +isolation. Also used as a simple transpiration driver. +""" +component FluxSource + "Water port" + port = HydraulicPort() + "Flux amplitude [g h^-1]" + parameter amplitude::Real = 5.0 + "Forcing period [h]" + parameter period::Real = 24.0 +relations + port.F = amplitude * sin(2 * π * time / period) +end + +""" +Non-growing environmental compartment (the `environmental_module`). + +Represents a fixed-size water pool (soil or air) subject to hydraulic laws but +without growth. The total water potential follows the empirical soil relation +Psi(W_r) = -(a / W_r) exp(-b W_r), with W_r the relative water content. +A large water capacity makes it act as a near-constant-potential reservoir. +""" +component EnvironmentalCompartment + "Water port" + port = HydraulicPort() + "Water capacity [g]" + parameter W_max::Real = 1e6 + "Initial relative water content [g g^-1]" + parameter W_r0::Real = 0.8 + "Soil-curve scale parameter [MPa]" + parameter a::Real = 0.03 + "Soil-curve shape parameter" + parameter b::Real = 0.5 + + "Water content [g]" + variable W::Real + "Relative water content [g g^-1]" + variable W_r::Real + "Total water potential [MPa]" + variable Psi::Real +relations + initial W = W_r0 * W_max + W_r = W / W_max + Psi = -(a / W_r) * exp(-b * W_r) + der(W) = port.F + port.Psi = Psi +end + +""" +Hydraulic connection (edge module). + +Darcy water flow between two compartments driven by the water-potential +difference: F = K (Psi_a - Psi_b), directed from port_a to port_b. +""" +component HydraulicConnection + "Port on the upstream (higher-potential) compartment" + port_a = HydraulicPort() + "Port on the downstream compartment" + port_b = HydraulicPort() + "Hydraulic conductivity [g h^-1 MPa^-1]" + parameter K::Real = 10.0 + "Water flow from a to b [g h^-1]" + variable F::Real +relations + F = K * (port_a.Psi - port_b.Psi) + port_a.F = F + port_b.F = -F +end + +""" +Transpiration boundary (leaf-air edge module). + +Draws a non-negative, diurnal water flux out of the connected compartment, +representing transpirational water loss: +F = Emax (1 - cos(2 pi t / period)) / 2, zero at midnight and peaking at midday. +""" +component Transpiration + "Water port (connects to a leaf compartment)" + port = HydraulicPort() + "Peak transpiration rate [g h^-1]" + parameter Emax::Real = 1.0 + "Diurnal period [h]" + parameter period::Real = 24.0 +relations + port.F = Emax * (1.0 - cos(2 * π * time / period)) / 2.0 +end + +# --- Increment 1 test: single compartment driven by an oscillating flux --- + +component TestCompartment + comp = HydraulicCompartment() + src = FluxSource(amplitude = 0.2, period = 24.0) +relations + connect(comp.port, src.port) +end + +analysis TestCompartmentTransient + extends TransientAnalysis(stop = 48.0) + model = TestCompartment() +end + +# --- Increment 2 test: compartment fed from a soil reservoir via Darcy flow --- + +component TestSoilCompartment + soil = EnvironmentalCompartment() + conn = HydraulicConnection(K = 10.0) + comp = HydraulicCompartment() +relations + connect(soil.port, conn.port_a) + connect(conn.port_b, comp.port) +end + +analysis TestSoilCompartmentTransient + extends TransientAnalysis(stop = 48.0) + model = TestSoilCompartment() +end + +# --- Increment 3 test: soil -> stem -> leaf chain driven by transpiration --- +# Reproduces the tomato-example behaviour: transpiration lowers stem water potential. + +component TestPlant + "Transpiration peak rate [g h^-1] (raise for stronger evaporative demand)" + parameter Emax::Real = 1.0 + + soil = EnvironmentalCompartment() + conn_ss = HydraulicConnection(K = 10.0) + stem = HydraulicCompartment(Rd0 = 0.5, L0 = 10.0) + conn_sl = HydraulicConnection(K = 10.0) + leaf = HydraulicCompartment(Rd0 = 0.4, L0 = 4.0) + transp = Transpiration(Emax = Emax, period = 24.0) +relations + connect(soil.port, conn_ss.port_a) + connect(conn_ss.port_b, stem.port) + connect(stem.port, conn_sl.port_a) + connect(conn_sl.port_b, leaf.port) + connect(leaf.port, transp.port) +end + +analysis TestPlantTransient + extends TransientAnalysis(stop = 48.0) + model = TestPlant() +end diff --git a/viz_submission/_data.json b/viz_submission/_data.json new file mode 100644 index 0000000..3aae66d --- /dev/null +++ b/viz_submission/_data.json @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/viz_submission/index.html b/viz_submission/index.html new file mode 100644 index 0000000..ced0a8c --- /dev/null +++ b/viz_submission/index.html @@ -0,0 +1,996 @@ + + + + + +PlantModules · Hydraulic Telemetry + + + + + + +
+ + +
+
+

01 · HYDRAULIC TELEMETRY

+

Water climbs the plant
soil → stem → leaf, over two days

+

An acausal PlantModules chain: a soil reservoir feeds a growing stem and leaf + through Darcy links while diurnal transpiration pulls water out of the canopy. Turgor, + water potential and Lockhart growth all respond to one driver — the sun.

+
+
+ Model + TestPlant · 48 h +
+
+ + +
+
+
+

02 · SYSTEM SCHEMATIC

+
+ Turgor fill + Water flux + Node size ∝ volume +
+
+
+ + + 12.0h +
+
+
+ + + + + + + + + + ROOT ZONE + + + + + + 0.72 + 0.60 + 1.00 + + + + + SOIL + Ψ −0.025 + + + + + STEM + 10.13 cm³ + Ψ −0.146 + + + + + LEAF + 2.48 cm³ + Ψ −0.249 + + + + + AIR + EFFLUX → SKY + +
+
+
Soil → stem flux0.72g/h
+
Stem → leaf flux0.60g/h
+
Stem turgor0.60MPa
+
Leaf turgor0.49MPa
+
+
+ +
+ + +
+

03 · STEM GROWTH

+
+165.8%
+

Stem volume 7.85 → 20.88 cm³ in 48 h. + Water uptake outruns the daily transpiration deficit, so the compartment + ratchets outward every cycle.

+
+ +
+
+ + +
+
+
+

04 · WATER POTENTIAL TRACE

+
+ Soil Ψ + Stem Ψ + Leaf Ψ +
+
+ Hover / scrub → +
+
+ +
+
+
+ Cursor time + 12.0h +
+
+ Soil Ψ + -0.025MPa +
+
+ Stem Ψ + -0.146MPa +
+
+ Leaf Ψ + -0.249MPa +
+
+
+ + +
+

05 · LEAF TURGOR

+
0.49MPa
+

Pressure that inflates the cell. It sags at midday as the leaf + loses water faster than the stem resupplies it.

+
+
0.45WINDOW · MPa0.70
+
+ + +
+
+
+

06 · GROWTH TRAJECTORY

+
+ Stem V + Leaf V +
+
+
+
+ +
+
+
+ Stem volume + 9.07cm³ +
+
+ Leaf volume + 2.30cm³ +
+
+
+ + +
+
+
+

07 · TRANSPIRATION DRIVER

+
+ Leaf efflux +
+
+ The sun · one damped cursor drives all four tiles +
+
+ +
+
+
+ Flux now + 1.00g/h +
+
+ Total 48 h + 24.0g +
+
+
+ + +
+

08 · RUN SUMMARY

+
+
Leaf growth+126.6%
+
Peak transpiration1.00g/h
+
Leaf Ψ minimum-0.261MPa
+
Soil Ψ (reservoir)-0.025MPa
+
Diurnal period24.0h
+
+
+ +
+ +
+ COMPETITION | PlantModules + JULIACON 2026 +
+ +
+ + + + From 055ea2949dcb1073f9ebb7b5db04e157e871c96b Mon Sep 17 00:00:00 2001 From: michielstock Date: Mon, 10 Aug 2026 12:33:44 +0200 Subject: [PATCH 2/2] :ambulance: standalone html --- viz_submission/index.html | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/viz_submission/index.html b/viz_submission/index.html index ced0a8c..ca73a38 100644 --- a/viz_submission/index.html +++ b/viz_submission/index.html @@ -4,9 +4,14 @@ PlantModules · Hydraulic Telemetry - - - +