Module Reference

Complete reference for all Fortran modules in the Canopy-App system. This page provides an overview and links to the detailed auto-generated API documentation.

Auto-Generated Documentation

For detailed API documentation with function signatures, parameters, and examples, see the Auto-Generated Doxygen API.

Core System Modules

Main Application

::: canopy selection: members: - canopy_app rendering: show_source: true show_bases: false heading_level: 4

The main program entry point that coordinates all model execution phases.

Memory Management

::: canopy selection: members: - MemoryManagement rendering: show_source: true show_bases: false heading_level: 4

Dynamic memory allocation and deallocation for all model arrays.

Reads and parses Fortran namelist configuration files.

Supported Namelists: - &canopy_inputs - Input/output file specifications - &canopy_options - Physics options and switches - &canopy_physics - Physical parameter settings

canopy_files_mod.F90

File Management

Utilities for file path handling, existence checking, and format detection.

Key Functions:

Complete NetCDF file handling for both input and output operations.

canopy_aero_ddep_mod.F90

Aerosol Dry Deposition

Sub-canopy aerosol dry deposition velocity calculations following Katul et al. (2010) and urban/non-vegetated dry deposition using Pleim et al. (2022).

Key Variables: - ddep_aero(nlon, nlat, modlays) - Vegetated aerosol dry deposition velocity profile (m/s)

User Options: - ifcanaeroddep - Logical switch in the namelist to enable/disable aerosol dry deposition calculations. When .TRUE., activates both vegetated and urban/non-vegetated routines and outputs (see ddep_aero variables). - aeroddep_opt - Integer option to select resistance parameterization for sub-canopy aerosol dry deposition: - 0: Katul et al. (2010) [default] - 1: Zhang et al. (2001) - 2: Petroff et al. (2008) - aeroddep_diam - Aerosol particle diameter (m) - aeroddep_rho - Aerosol particle density (kg/m^3)

Subroutines: - canopy_aero_ddep_katul2010 - Vegetated (Katul et al. 2010) - canopy_aero_ddep_pleim2022 - Urban/non-vegetated (Pleim et al. 2022) Capabilities: - Read meteorological input data - Write model output in CF-compliant format - Handle time series and profile data - Error checking and validation

canopy_txt_io_mod.F90

Text File Input/Output

ASCII text file I/O operations for simple data exchange.

Features: - Column-based data reading - Formatted output generation - Header processing - Quality control checks

Physical Process Modules

canopy_canmet_mod.F90

Canopy Meteorology

Computes meteorological variables within and above the canopy.

Calculations: - Wind speed profiles using similarity theory - Temperature and humidity gradients - Atmospheric stability corrections - Turbulent mixing parameterizations

Key Variables: - wind_prof(nlev) - Wind speed profile - temp_prof(nlev) - Temperature profile - rh_prof(nlev) - Relative humidity profile

canopy_rad_mod.F90

Radiation Transfer

Solar and longwave radiation calculations through the canopy.

Capabilities: - Beer's law attenuation - Direct and diffuse radiation separation - Solar zenith angle calculations - Photosynthetically active radiation (PAR)

Key Variables: - solar_flux(nlev) - Solar radiation by level - par_flux(nlev) - PAR availability - zenith_angle - Solar zenith angle

canopy_bioemi_mod.F90

Biogenic Emissions

Vegetation emissions of volatile organic compounds.

Emission Types: - Temperature-dependent emissions (monoterpenes) - Light-dependent emissions (isoprene) - Stress-induced emissions - Species-specific emission factors

Key Variables: - emis_isop(nlev) - Isoprene emission rates - emis_mono(nlev) - Monoterpene emission rates - emis_total - Total canopy emissions

canopy_drydep_mod.F90

Dry Deposition

Removal of atmospheric gases and particles by vegetation.

Methods: - Multi-layer resistance networks - Big-leaf approximations - Stomatal and cuticular pathways - Environmental controls

Key Variables: - vdep_gas(nspec) - Deposition velocities by species - flux_dep(nspec) - Deposition fluxes - resist_stom(nlev) - Stomatal resistance

canopy_phot_mod.F90

Photolysis Rates

Photolysis rate calculations for atmospheric chemistry.

Features: - Actinic flux attenuation - Species-specific cross sections - Canopy shading effects - Wavelength-dependent calculations

Key Variables: - jvals(nphot,nlev) - Photolysis rates by species and level - actinic_flux(nlev) - Actinic flux profile

Supporting Modules

canopy_const_mod.F90

Physical Constants

Fundamental physical and mathematical constants used throughout the model.

Categories: - Physical constants (gravity, gas constant, etc.) - Conversion factors - Mathematical constants - Default parameter values

canopy_utils_mod.F90

Utility Functions

General-purpose utility functions and mathematical operations.

Functions: - Array operations and statistics - Unit conversions - Mathematical utilities - String processing

canopy_coord_mod.F90

Coordinate Systems

Coordinate system transformations and grid utilities.

Features: - Vertical coordinate transformations - Grid spacing calculations - Level interpolation routines

canopy_date_mod.F90

Date and Time Handling

Date/time parsing, validation, and calculations.

Capabilities: - Date string parsing - Julian day calculations - Time zone handling - Solar angle computations

Variable and Parameter Modules

canopy_canvars_mod.F90

Canopy Variables

Central repository for all canopy-related variables and arrays.

canopy_canopts_mod.F90

Canopy Options

Model configuration options and physics switches.

canopy_bioparm_mod.F90

Biogenic Parameters

Parameters for biogenic emission calculations.