Meteorology

`meteo.csv`

The meteorology file is used to input variables related to the environment. It is a file prepared in the CSV format where each column is a variable, and each line is a time step. A time step is a given period of time, it can be a period of 1 minute or a period of 100 days (but see the section about that below).

File format

The file is a CSV file (semicolon separated) enriched by optional parameters as comments in the header (and following the YAML format).

You can download an example file here:

Attachments

meteo.csv (0 kb)

The file is structured as follows:

#' name: Aquiares
#' latitude: 15.0  # in degrees
#' altitude: 100.0 # in meters
#' use : relativeHumidity clearness
date;hour_start;hour_end;temperature;relativeHumidity;VPD;clearness;Re_SW_f;wind;atmosphereCO2_ppm
2016/06/12;12:00:00;12:30:00;25;60;150;0.75;500;1;380
2016/06/12;12:30:00;13:00:00;26;62;150;0.75;500;1.5;380
2016/06/12;13:00:00;13:30:00;25.3;58;150;0.75;500;1.5;380

The four lines at the beginning are YAML-formatted metadata used as input parameters for ARCHIMED-φ. They define properties of the site where the data was measured. The first one is the name of the site (completely free), then comes its latitude (degrees) and altitude (meters). The use parameter defines which column is used when several related (i.e. concurrent) variables are defined in the data. In our example the relativeHumidity and the VPD are declared, and the user must choose which one to use.

The first line after the commented lines defines the column names. These names are all fixed and should be matched exactly (ARCHIMED-φ is case-sensitive).

Here is a table summarizing the information about those variables:

Variable	Unit	Description	If.missing	Example
date	Y/m/d	Date of the time step	mandatory	2020/09/17
hour_start	H:M:S	Beginning of the time step	mandatory	12:00:00
hour_end	H:M:S	End of the time step	use step_duration	12:30:00
step_duration	seconds	Time step duration	use hour_end	1800
temperature	Celsius	Air temperature (above canopy)	mandatory	25
relativeHumidity	%	Air relative humidity (above canopy)	use VPD	60
VPD	hPa	Air vapor pressure deficit (above canopy)	use rh	2
wind	m s-1	wind speed (above canopy)	mandatory	1.5
clearness	%	Sky clearness	*	0.6
Ri_SW_f	W m-2	Incoming short wave radiation flux	*	500
Ri_PAR_f	W m-2	Incoming PAR radiation flux	*	500
Ri_NIR_f	W m-2	Incoming NIR radiation flux	*	500
Ri_TIR_f	W m-2	Incoming TIR radiation flux	computed from temperature	500
Ri_xxx_f	W m-2	Incoming radiation flux for custom waveband	optional	500
atmosphereCO2_ppm	ppm	Air CO2 concentration	Use constant	420

* see sections below

Variables details

Light

The date and hours are used to compute the sun position in the sky for the computation of the light interception.

The clearness, Ri_SW_f, Ri_PAR_f, Ri_NIR_f, and Ri_xxx_f are also related to the light interception computation.

The total energy coming from solar radiation at earth surface is mainly between 400 and 2500-3000 nm (see Fig. 1).

Fig. 1: Solar irradiance spectrum above atmosphere and at earth surface. Source: wikimedia

The spectrum of incoming solar radiation is simplified into two wavebands in ARCHIMED-φ:

Ri_PAR_f is the photosynthetically active radiation flux coming from the atmosphere. It typically ranges from 400 to 700 nm (i.e. visible part of the light), and is the radiation primarily used for plant photosynthesis.
Ri_NIR_f is the Near Infrared radiation flux coming from the atmosphere. It typically ranges from 700 to 3000 nm and is more precisely defined by the sum of the NIR and SWIR wavebands.

These two wavebands represent the short wave radiation flux coming from the atmosphere. And their sum gives Ri_SW_f, with the PAR radiation representing typically 48% and the NIR 52%.

The long wave radiation (TIR, i.e. thermal infrared) is the radiation emitted by any object due to its surface temperature. It is possible to provide the TIR coming from the atmosphere as an input to ARCHIMED-φ by providing the Ri_TIR_f variable.

These variables are not necessarily measured, so ARCHIMED-φ provides a simpler way to parameterize the incoming radiation by using a simpler variable: the clearness. Indeed, it is simple to compute the extraterrestrial solar radiation (i.e. the radiation in yellow in Fig. 1) at a given location and time, but this radiation is partly absorbed, diffused and reflected by the atmosphere before getting to the ground. These effects are mainly driven by the composition of the atmosphere, which can be approximated (coarsely) by the clearness of the sky, i.e. the opposite of the cloud cover in the sky. It ranges from 0 (sky full of clouds) to 1 (clear sky), but values rarely goes below 0.2 or above 0.8.

If any of these variable is missing, the model computes it, provided at least one of the clearness, Ri_SW_f, Ri_PAR_f, Ri_NIR_f is given. Please keep in mind the more variables are provided as inputs, the lower the simulation error because it is preferable to measure a variable than simulating it.

The user can also input any custom waveband for the incoming light using the “Ri_xxx_f” naming convention, e.g. for the red band: Ri_red_f. These custom wavebands can be used to compute the light interception and scattering for any waveband, but they don’t participate to the energy balance nor the photosynthesis (the shortwave is already computed using PAR and NIR).

The custom wavebands must be part of the shortwave band (PAR and NIR), and the optical properties of the components in the scene must be provided (see this section for more information).

Micro-environment

The temperature, relativeHumidity, VPD, wind and atmosphereCO2_ppm are used for the biophysical computations, such as the energy balance and photosynthesis.

If the relativeHumidity is not given, the model uses the VPD, but one or the other must be provided. If the atmosphereCO2_ppm is not given in the meteo file, it is read from the constant parameter file (const.yml, see this section for more details).

Some thought on time steps duration

The duration of a time step is up to the user, and mainly depends on the use-case, the variables requested and the precision needed. Shorter time-steps tends to give best results because they allow to better integrate non-linear processes that are not well integrated otherwise (e.g. a rapid change in the incoming radiation on a leaf can impact greatly its energy balance).

In general we recommend time-steps of maximum 30-minutes for simulations with biophysical processes (e.g. photosynthesis, energy balance, transpiration). This is based on the assumption that these variables can be safely considered at steady-state at or below a 30-minute time range.

If only the light interception is needed, the time step can be much larger because the model use the true position of the sun every radiation_timestep (parameter from the configuration file), and not every step in the meteorology file.

For all other variables, there is a trade-off between the duration of each step and their number to optimize both the predictions and computation time. For example if we need to simulate one day at 30-minute time-steps, it will require 48 time-steps in total, but only 24 with one hour time-steps. The latter simulation will be almost twice as fast as the former, but will probably lead to a greater simulation error compared to measurements.

The cache_radiation parameter can alleviate this effect though (parameter from the configuration file). It allows to compute the results of the light interception for each direction relative to the global radiation, and to cache the results for further use in other time-steps. It is generally admitted this parameter should be set to true when the number of time-steps to simulate is greater than the number of directions (due to overheads on computing the cached radiation).