MEGAN Biogenic Emissions¶

Overview¶

CECE provides two MEGAN biogenic emission schemes:

• megan — Single-species isoprene scheme (original, ported from HEMCO)
• megan3 — Full MEGAN3 multi-species, multi-class emission system with 19 emission classes, 5-layer canopy model, and chemical mechanism speciation

Both schemes coexist and can be selected independently via the YAML configuration.

MEGAN (Single-Species Isoprene)¶

The original scheme computes isoprene emissions using activity factors for LAI, temperature (light-dependent and light-independent pathways), PAR (via PCEEA), leaf age, soil moisture, and CO₂ inhibition. Ported from HEMCO's hcox_megan_mod.F90.

Registration Names¶

• Native C++: "megan"
• Fortran bridge: "megan_fortran"

Configuration¶

physics_schemes:
  - name: megan
    options:
      beta: 0.13
      ldf: 1.0
      aef: 1.0e-9
      co2_concentration: 400.0

Import Fields¶

Export Fields¶

MEGAN3 (Multi-Species, Multi-Class)¶

The full MEGAN3 scheme computes emissions for 19 biogenic emission classes, applies a comprehensive set of gamma factors including a 5-layer canopy model, and converts class totals to mechanism-specific output species via a configurable speciation engine.

Registration Names¶

• Native C++: "megan3"
• Fortran bridge: "megan3_fortran"

19 Emission Classes¶

Gamma Factors¶

For each emission class, the scheme computes:

• γ_T_LI — Light-independent temperature response (exponential β formulation)
• γ_T_LD — Light-dependent temperature response (Guenther et al. 2012)
• γ_PAR — PAR response via PCEEA algorithm
• γ_LAI — Leaf area index correction
• γ_age — Leaf age (new/growing/mature/old fractions)
• γ_SM — Soil moisture
• γ_CO₂ — CO₂ inhibition (Possell or Wilkinson)
• γ_stress — Wind/temperature/air quality stress (optional)

Combined via LDF partitioning:

emission[class] = NORM_FAC × AEF × γ_LAI × γ_age × γ_SM × γ_CO₂ × [(1-LDF)×γ_T_LI + LDF×γ_PAR×γ_T_LD] × γ_stress

Canopy Model (MEGCANOPY)¶

A 5-layer Gaussian quadrature canopy model computes: - Beer-Lambert PAR extinction through the canopy - Sunlit/shaded leaf fractions at each layer - Leaf temperature via energy balance - Canopy-integrated emission activity factor

All light-dependent factors are zero when solar cosine ≤ 0 (nighttime).

Speciation¶

After computing 19 class totals, the speciation engine converts them to mechanism-specific output species using scale factors from a YAML MAP file:

output[species] = (Σ class_total[c] × scale_factor[c→s]) × MW[s]

See Speciation Configuration below for the YAML format.

Soil NO Handling¶

The NO emission class reads soil_nox_emissions from the export state (produced by the BDSNP module or any other soil NO scheme). If the field is missing, a warning is logged and NO is set to zero.

Configuration¶

physics_schemes:
  - name: bdsnp
    options:
      soil_no_method: bdsnp
  - name: megan3
    options:
      mechanism_file: data/speciation/spc_cb6.yaml
      speciation_file: data/speciation/map_cb6.yaml
      speciation_dataset: MEGAN
      co2_concentration: 415.0
      co2_method: possell
      enable_wind_stress: false
      enable_temp_stress: false
      emission_classes:
        ISOP:
          ldf: 0.9996
          ct1: 95.0
          cleo: 2.0
          beta: 0.13
          anew: 0.05
          agro: 0.6
          amat: 1.0
          aold: 0.9
          default_aef: 1.0e-9
        MT_PINE:
          ldf: 0.10
          ct1: 80.0
          cleo: 1.83
          beta: 0.10
          anew: 2.0
          agro: 1.8
          amat: 1.0
          aold: 1.05
          default_aef: 3.0e-10
        # ... remaining classes
    input_mapping:
      temperature: T2M
      leaf_area_index: LAI
      par_direct: PARDR
      par_diffuse: PARDF
      solar_cosine: COSZS
      soil_moisture_root: GWETROOT
      wind_speed: U10M
    output_mapping:
      MEGAN_ISOP: ISOP_BIOG
      MEGAN_TERP: TERP_BIOG

Import Fields¶

Export Fields¶

Dynamic — one field per mechanism species with MEGAN_ prefix:

Speciation Configuration¶

MEGAN3 uses two YAML files for chemical mechanism speciation:

SPC File (Mechanism Species)¶

Defines the target mechanism species and their molecular weights. Uses the MICM/OpenAtmos format:

name: CB6_AE7
species:
  - name: ISOP
    molecular weight [kg mol-1]: 0.06812
  - name: TERP
    molecular weight [kg mol-1]: 0.13623
  - name: PAR
    molecular weight [kg mol-1]: 0.01443
  # ... up to 36 species for CB6

MAP File (Speciation Mappings)¶

Defines how the 19 MEGAN emission classes map to mechanism species with per-class scale factors. Uses a dataset-oriented format that supports multiple emission sources:

mechanism: CB6_AE7
datasets:
  MEGAN:
    ISOP:
      ISOP: 1.0
    TERP:
      MT_PINE: 0.5
      MT_ACYC: 0.3
      MT_CAMP: 0.1
      MT_SABI: 0.05
      MT_AROM: 0.05
    MEOH:
      MEOH: 1.0
    SESQ:
      SQT_HR: 0.7
      SQT_LR: 0.3
    "NO":
      "NO": 1.0
    CO:
      CO: 1.0

Each entry under a mechanism species name lists the contributing emission classes and their fractional scale factors. The speciation engine computes:

output[TERP] = (class_total[MT_PINE] × 0.5 + class_total[MT_ACYC] × 0.3 + ...) × MW[TERP]

Supported Mechanisms¶

CECE ships with speciation files for:

To switch mechanisms at runtime, change mechanism_file and speciation_file in the YAML config — no recompilation needed.

Adding a New Mechanism¶

1. Create an SPC file with species names and molecular weights (kg/mol)
2. Create a MAP file with a MEGAN dataset section mapping emission classes to your mechanism species
3. Point mechanism_file and speciation_file to your new files

Scheme Ordering¶

BDSNP must run before MEGAN3 so that soil_nox_emissions is available:

physics_schemes:
  - name: bdsnp        # Runs first, writes soil_nox_emissions
  - name: megan3       # Runs second, reads soil_nox_emissions for NO class