Output Files

The Canopy-App model generates various output files containing simulation results. This section describes the format and content of each output file type.

Output File Types

NetCDF Output Files

The model generates netCDF files with comprehensive simulation results:

Primary Output File: `canopy_output.nc`

Contains the main simulation variables:

Dimensions: - time: Number of time steps - lev: Number of vertical levels - lat: Number of latitude points - lon: Number of longitude points

Example Canopy-Process Variables:

Variable	Description	Units	Dimensions
`time`	Time coordinate	hours since start	(time)
`lev`	Vertical level coordinate	m	(lev)
`lat`	Latitude coordinate	degrees_north	(lat)
`lon`	Longitude coordinate	degrees_east	(lon)
`canwind`	Canopy winds	m/s	(time,lev,lat,lon)
`kz`	Canopy eddy diffusivities	kg/kg	(time,lev,lat,lon)
`rjcf`	Canopy photolysis attenuation factors		(time,lev,lat,lon)
`emi_isop`	Biogenic emissions	kg/m3 s	(time,lev,lat,lon)
`ddep_o3`	Ozone dry deposition	cm/s	(time,lev,lat,lon)
---------------------------------------------------------------------------------------------

Example Canopy-Specific Variables

Text Output Files

For simple analysis, the model can output text files:

Point Output: `point_file_YYYYMMDD.sfcfXXX.txt`

Contains time series data for single points:

# Example Canopy-App Point Output for Canopy Winds
#    time stamp: 2022-07-01-11:00:00.0000
#    reference height, h:   10.0 m
#    number of model layers:    100
#    lat      lon  height (m)  LAD (m2 m-3)       ws (m s-1)
      34.97   270.00      0.00        0.00  0.0000000E+00
      34.97   270.00      0.50        0.08  5.9679881E-02
      34.97   270.00      1.00        0.13  7.8142006E-02
    ...

Example 3D Canopy Variables for Input PAVD: `point_file_canvars_YYYYMMDD.sfcfXXX.txt`

Emission Rates

Example biogenic emission rates:

Variable	Description	Units	Dimensions
`emi_isop`	Isoprene emission rate	kg/m²/s	(time,lev,lat,lon)
`emi_mono`	Monoterpene emission rate	kg/m²/s	(time,lev,lat,lon)
`emi_sesq`	Sesquiterpene emission rate	kg/m²/s	(time,lev,lat,lon)
`emi_ovoc`	Other VOC emission rate	kg/m²/s	(time,lev,lat,lon)

import netCDF4 as nc
import numpy as np
import matplotlib.pyplot as plt

# Open output file
ds = nc.Dataset('canopy_output.nc', 'r')

# Read variables
time = ds.variables['time'][:]
temp = ds.variables['temp'][:]
lai = ds.variables['lai'][:]

# Plot results
plt.figure(figsize=(10, 6))
plt.plot(time, temp[:, 0, 0, 0])
plt.xlabel('Time (hours)')
plt.ylabel('Temperature (K)')
plt.title('Surface Temperature')
plt.show()

ds.close()

NCO (NetCDF Operators)

Command-line tools for netCDF manipulation:

# Extract variable
ncks -v temp canopy_output.nc temp_only.nc

# Time average
ncwa -a time canopy_output.nc canopy_avg.nc

# Spatial subset
ncks -d lat,40.0,41.0 -d lon,-81.0,-80.0 canopy_output.nc subset.nc

CDO (Climate Data Operators)

Advanced climate data operations:

# Time series statistics
cdo timstd canopy_output.nc temp_std.nc
cdo timmean canopy_output.nc temp_mean.nc

# Vertical interpolation
cdo intlevel,850,500,300 canopy_output.nc levels.nc

Output Customization

Namelist Options

Control output through namelist parameters:

&CANOPY_OPTIONS
 ! Output format (1=netCDF, 2=text)
 outfmt_opt = 1

/

Choose specific variables for output:

&OUTPUT_CONTROL
 ! Meteorological variables
 out_temp = .true.
 out_qv = .true.
 out_wind = .true.
 out_tke = .true.

 ! Canopy variables
 out_ppfd = .true.
 out_tleaf = .true.
 out_gsw = .true.

 ! Chemical variables
 out_chem = .false.
/

Quality Control

The model performs output validation:

Range checks: Ensures values are physically reasonable
Conservation checks: Verifies mass and energy conservation
Metadata validation: Confirms proper units and attributes
Format compliance: Ensures CF convention compliance

For troubleshooting output issues, see the Troubleshooting Guide.