OpenWQ
BGC Templates Library
Pre-built biogeochemical reaction frameworks for NATIVE_BGC_FLEX and PHREEQC
— ready to use, easy to customize
— ready to use, easy to customize
Contents
• Templates Library Overview
Section 01: Individual Chemicals
• Nitrogen & Phosphorus Templates
• Dissolved Oxygen & Carbon
• Phytoplankton/Algae Dynamics
• Plant Uptake Module
• Emerging Contaminants
• Groundwater Age Tracking
• New Advanced Templates
Section 02: Popular Model Frameworks
• SWAT, QUAL2K, HYPE, WASP8
Section 03: Thermodynamic Templates
• FT Factor Templates
• Redox Ladder
Section 04: PHREEQC Templates
• Equilibrium Templates
• Kinetic Templates (.pqi)
• Template Summary
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Templates Library Overview
🧪 NATIVE_BGC_FLEX Templates
JSON-based kinetic reaction frameworks
- Individual Chemicals — N, P, C, DO, metals
- Popular Models — SWAT, QUAL2K, HYPE, WASP8
- Thermodynamic — Redox ladder, diagenesis
- v2.0 New — Algae, plant uptake, PFAS
⚗️ PHREEQC Templates
Equilibrium + kinetic geochemistry (.pqi)
- Equilibrium — Major ions, minerals
- v2.0 Kinetic — DO, algae, plant uptake, ECs
Location:
supporting_scripts/Model_Config/config_support_lib/BGC_templates/
How to Use
- Select template(s) for your application
- Copy to your project folder
- Customize parameters as needed
- Reference in master config
Tip: Templates can be merged! Combine species and frameworks from multiple templates.
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01
Individual Chemicals
Nitrogen & Phosphorus Templates
nitrogen_simple.json
Basic 3-pool nitrogen cycle
- NH₄ ↔ NO₃ ↔ N₂
- Mineralization, nitrification, denitrification
- Temperature-dependent (Q10)
nitrogen_full.json
Complete N cycle with advanced processes
- O₂ limitation on all reactions
- N₂O emissions pathway
- Plant uptake with seasonal dynamics
- Immobilization under high C:N
phosphorus_simple.json
Basic 3-pool phosphorus cycle
- SRP ↔ Organic-P ↔ Particulate-P
- Mineralization, sorption
phosphorus_full.json
Full P cycle with redox control
- Fe-bound P release under anoxia
- Sediment P flux
- Labile vs refractory pools
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Dissolved Oxygen & Carbon v2.0
dissolved_oxygen.json Updated
Complete DO budget with 12 transformations
🌊
Reaeration
4 formulas (Owens, O'Connor-Dobbins...)
🌿
Photosynthesis
Steele light model
🔥
BOD decay
Fast + slow fractions
⚗️
NOD
4.57 mg O₂/mg NH₄-N
🏔️
SOD
Sediment oxygen demand
carbon_organic.json
DOC/POC cycling
- DOC mineralization → CO₂
- POC hydrolysis → DOC
- Photochemical degradation
- Flocculation (DOC → POC)
DO_BALANCE_SIMPLE — Included framework for Streeter-Phelps screening (3 transformations)
// Reaeration example (O'Connor-Dobbins) "kinetics": [ "(ka_20 * 1.024^(T-20)) * (DO_sat - DO)", "mg-O2/L/day" ]
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Phytoplankton/Algae Dynamics v2.0 NEW
phytoplankton_algae.json
WASP8-style eutrophication model — 11 transformations
| Process | Description |
|---|---|
| Growth | Light (Steele) + Nutrient (MM) |
| N uptake | Preferential NH₄, then NO₃ |
| P uptake | Redfield C:N:P = 106:16:1 |
| Respiration | Temperature-dependent |
| Mortality | Non-predatory death |
| Settling | Gravitational sinking |
| Grazing | Zooplankton (Ivlev model) |
8 Chemical Species:
PHYTO, ZOO, Chla, NO3_N, NH4_N, PO4_P, DOC, DO
PHYTO, ZOO, Chla, NO3_N, NH4_N, PO4_P, DOC, DO
// Steele photoinhibition model "kinetics": [ "mu_max * PHYTO * (I/I_opt) * exp(1 - I/I_opt) * (TIN/(Ks_N + TIN)) * (PO4_P/(Ks_P + PO4_P)) * theta^(T - 20)" ] // Ivlev grazing formulation "kinetics": [ "g_max * ZOO * (1 - exp(-lambda * PHYTO))" ]
Chlorophyll-a proxy: Chla:C ratio for biomass tracking
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Plant Uptake Module v2.0 NEW
plant_uptake.json
SWAT/HYPE-style vegetation cycling — 3 frameworks, 15 transformations
PLANT_UPTAKE_FULL (8 transforms)
- NO₃ uptake — Mobile, easily transported
- NH₄ uptake — Preferred (less energy cost)
- PO₄ uptake — Diffusion-limited
- Senescence — Litterfall with retranslocation
- Litter N/P/C mineralization
RIPARIAN_BUFFER (3 transforms)
- Enhanced NO₃ uptake in riparian zone
- Denitrification in saturated soil
- P retention via sedimentation
Seasonal Modulation:
f_season = sin(π × (DOY - 60) / 240) for growing season
f_season = sin(π × (DOY - 60) / 240) for growing season
// NO3 uptake with seasonal factor "kinetics": [ "k_uptake_no3 * NO3_N / (Ks_N + NO3_N + NH4_N) * f_growth * f_temp * f_moisture" ] // Litter N mineralization "kinetics": [ "k_litter_N * LITTER_N * theta^(T - 293)" ]
PLANT_UPTAKE_SIMPLE (4 transforms)
Lumped N and P uptake for screening models
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Emerging Contaminants v2.0 NEW
emerging_contaminants.json
Micropollutants framework — 6 cycling frameworks, 32 transformations
| Framework | Compounds | Transforms |
|---|---|---|
| PHARMACEUTICALS | Antibiotics, analgesics, hormones | 8 |
| PPCPS | Fragrances, UV filters, triclosan | 6 |
| PFAS | PFOA, PFOS, GenX | 5 |
| MICROPLASTICS | Fibers, fragments, beads | 6 |
| ENDOCRINE_DISRUPTORS | Estrogens, BPA | 4 |
| EMERGING_SIMPLE | Generic screening | 3 |
Key Processes:
- Biodegradation (T-dependent)
- Photolysis (light + depth)
- Sorption to sediments
- Volatilization (fragrances)
- Settling/aggregation (MPs)
// PFAS - extremely persistent "kinetics": [ "k_sorp_pfoa * PFAS_PFOA * (1 - PFAS_PFOA/Smax)" ] // Only sorption - no biodegradation! // Microplastic settling "kinetics": [ "v_settle * MP_fiber / depth" ]
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Groundwater Age Tracking v2.0 NEW
groundwater_age.json
Environmental tracers for residence time — 7 frameworks
| Tracer | Half-life | Age Range |
|---|---|---|
| ³H-³He (Tritium) | 12.32 yr | 0-50 years |
| CFC-11, CFC-12 | — | 1940s-1990s |
| SF₆ | — | Post-1990 |
| ¹⁴C | 5,730 yr | 100-40,000 yr |
Mean Age: Tracks water age directly (1 day/day accumulation)
// Tritium decay: 3H -> 3He "kinetics": [ "lambda_H3 * TRITIUM" ] // lambda = ln(2)/12.32yr = 0.0562/yr // 3H-3He apparent age // Age = ln(1 + 3He_trit/3H) / lambda // Carbon-14 age "kinetics": [ "lambda_C14 * CARBON14" ] // Age = -8267 × ln(14C/100)
Applications
- Aquifer vulnerability assessment
- Recharge rate estimation
- Flow path delineation
- Mixing model calibration
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New Advanced Templates v2.0 NEW
sediment_diagenesis.json
Multi-G OM, redox cascade, P/N cycling, CH₄
wetland_processing.json
N/P/TSS removal, k-C* design model
tile_drainage.json
NO₃ leaching, P transport, snowmelt flush
pH_alkalinity.json
Carbonate system, ALK budget, AMD
heavy_metals.json
Cu, Zn, Pb, Cd, Hg speciation and sorption
pathogens.json
E. coli, fecal coliforms, virus decay
pesticides.json
Generic pesticide fate with hydrolysis
silica.json
Dissolved silica for diatom modeling
iron_manganese.json
Fe/Mn redox cycling in sediments
All templates include:
- Complete
CHEMICAL_SPECIESdefinitions - Mobile species configuration
- Parameter values with literature-based ranges
- Inline documentation (underscore keys)
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Popular Model Frameworks
SWAT, QUAL2K, HYPE, WASP8 Frameworks
SWAT_full_nutrients.json
Complete SWAT-style N/P/C cycling
- 3 organic N pools (fresh, active, stable)
- 3 organic P pools
- Soil layer decomposition
- Erosion-linked P transport
QUAL2E_stream.json
Classic stream water quality
- DO-BOD dynamics
- Algae + nutrients
- SOD, reaeration
HYPE_nutrients.json
Nordic-style large-scale modeling
- Wetland retention processes
- Tile drainage N loss
- Snow-melt nutrient flush
WASP8_eutrophication.json
Lake/estuary eutrophication
- Multi-algae groups (diatoms, greens, cyano)
- Sediment diagenesis
- Zooplankton grazing
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Thermodynamic Templates
FT Factor Templates — Redox Ladder
| Template | ΔG° (kJ/mol) |
|---|---|
| aerobic_respiration.json | −125 |
| nitrification.json | −119 to −79 |
| denitrification_thermodynamic.json | −119 |
| anammox.json | −357 |
| manganese_reduction.json | −95 |
| iron_reduction.json | −50 |
| sulfate_reduction.json | −25 |
| methanogenesis.json | −20 |
full_sediment_diagenesis.json
Complete redox cascade — 13 reactions
Combines all TEAPs (Terminal Electron Accepting Processes) with automatic FT enforcement
// F_T auto-enforces redox sequence "kinetics": [ "k * X * (NO3/(Km+NO3)) * (DOC/(Km_DOC+DOC)) * (1 - exp(-((119-45)/(2*R*(T+273)))))" ] // ^^^^^ F_T term ^^^^^^
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PHREEQC Templates
PHREEQC Templates (.pqi files)
Equilibrium Templates
- major_ions_equilibrium.pqi
Ca, Mg, Na, K, Cl, SO₄, HCO₃ - nitrogen_speciation.pqi
NH₄/NH₃, NO₂, NO₃ with redox - phosphorus_minerals.pqi
PO₄ speciation + mineral SI - trace_metals.pqi
Fe, Mn, Cu, Zn complexation
Kinetic Templates v2.0
- dissolved_oxygen_kinetics.pqi
BOD, NOD, SOD with RATES - phytoplankton_kinetics.pqi
Algae growth, grazing - plant_uptake_kinetics.pqi
N/P uptake, litter cycling - emerging_contaminants_kinetics.pqi
Pharma, PFAS, EDCs - groundwater_age_kinetics.pqi
³H-³He, ¹⁴C, CFCs, SF₆ - sediment_diagenesis_kinetics.pqi
Multi-G OM, redox cascade - wetland_processing_kinetics.pqi
N/P/TSS/pathogens removal - tile_drainage_kinetics.pqi
NO₃ leaching, P transport - pH_alkalinity_kinetics.pqi
Carbonate, ALK, AMD
Note: Use NATIVE_BGC_FLEX for complex biological processes. PHREEQC kinetics best for coupled geochemical-biological systems.
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Template Summary
| Category | Templates | Key Features | Status |
|---|---|---|---|
| Nutrients | nitrogen, phosphorus (simple/full) | N & P cycling, plant uptake, redox | Stable |
| Dissolved Oxygen | dissolved_oxygen | 12 transforms, 4 reaeration formulas | v2.0 |
| Algae | phytoplankton_algae | Steele + MM, zooplankton, Chla | v2.0 |
| Vegetation | plant_uptake | 3 frameworks, riparian buffer | v2.0 |
| Micropollutants | emerging_contaminants | PFAS, PPCPs, microplastics, EDCs | v2.0 |
| Popular Models | SWAT, QUAL2K, HYPE, WASP8 | Complete model frameworks | Stable |
| Thermodynamic | 10 redox templates + diagenesis | FT factor, automatic ladder | Stable |
| Groundwater Age | groundwater_age | ³H-³He, ¹⁴C, CFCs, SF₆ tracers | v2.0 |
| Sediment Diagenesis | sediment_diagenesis | Multi-G OM, redox cascade, P/N cycling | v2.0 |
| Wetland/BMP | wetland_processing | N/P/TSS removal, k-C* model | v2.0 |
| Tile Drainage | tile_drainage | NO₃ leaching, P transport, snowmelt | v2.0 |
| pH/Alkalinity | pH_alkalinity | Carbonate system, ALK budget, AMD | v2.0 |
| PHREEQC | 4 equilibrium + 9 kinetic | Full geochemistry + bio processes | Mixed |
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