6.2 Model configuration

This page is used for basic model configuration, including when your model will run and what input data it will use.

6.2.1 Choosing meteorology

Once a Machine, Model, and Site have been selected, PEcAn will take you to the Input selection page. From this page you will select what Plant Functional Type (PFT) you want to run at a site, the start and end dates of the run, and various Input selections. The most common of these across all models is the need to specify meteorological forcing data. The exact name of the menu item for meteorology will vary by model because all of the Input requirements are generated individually for each model based on the MODEL_TYPE table. In general there are 3 possible cases for meteorology

  • PEcAn already has driver files in its database
  • PEcAn does not have drivers, but can generate them from publicly available data
  • You need (or want) to upload your own drivers

The first two cases will appear automatically in the the pull down menu. For meteorological files that already exist you will see the date range that’s available. By contrast, met that can be generated will appear as “Use ”, where is the origin of the data (e.g. “Use Ameriflux” will use the micromet from an Ameriflux eddy covariance tower, if one is present at the site).

If you want to upload your own met data this can be done in three ways.

  1. The default way to add met data is to incorporate it into the overall meteorological processing workflow. This is preferred if you are working with a common meteorological data product that is not yet in PEcAn’s workflow. This case can be divided into two special cases:

    1. Data is in a common MIME-type that PEcAn already has a converter for (e.g. CSV). In this case you’ll want to create a new Format record for the meta-data so that the existing converter can process this data. See documentation for [Creating a new Format record in BETY] for more details.

    2. Data is in a more complicated format or interactive database, but large/useful enough to warrent a custom conversion function. Details on creating custom met conversions is in the [Input Conversion], though at this stage you would also be strongly encouraged to contact the PEcAn development team.

  2. The second-best way is to upload data in PEcAn’s standard meteorological format (netCDF files, CF metadata). See [Input Conversion] for details about variables and units. From this standard, PEcAn can then convert the file to the model-specific format required by the model you have chosen. This approach is preferred for a rare or one-off meterological file format, because PEcAn will also be able to convert the file into the format required by any other model as well.

  3. The last option for adding met data is to add it in a model-specific format, which is often easiest if you’ve already been running your model at a site and are just switching to using PEcAn.

6.2.2 Met workflow

In a nutshell, the PEcAn met workflow is designed to reduce the problem of converting n possible met inputs into m possible model formats, which requires n x m conversion functions as well as numerous custom functions for downscaling, gap filling, etc. Instead, PEcAn works with a single met standard, and thus requires n conversion functions, one for converting each data source into the PEcAn standard, and then m conversion functions for converting from that standard to what an individual model requires. For a new model joining the PEcAn system the burden in particularly low – writing one conversion function provides access to n inputs. Similarly, PEcAn performs all other operations/manipulations (extracting a site, downscaling, gap filling, etc) within the PEcAn standard, which means these operations only need be implemented once.

Consider a generic met data product named MET for simplicity. PEcAn will use a function, download.MET, to pull data for the selected year from a public data source (e.g. Ameriflux, North American Regional Reanalysis, etc). Next, PEcAn will use a function, met2CF.MET, to convert the data into the PEcAn standard. If the data is already at the site scale it will then gapfill the data. If the data is a regional or global data product, PEcAn will then permute the data to allow easier site-level extraction, then it will extract data for the requested site and data range. Modules to address the temporal and spatial downscaling of meteorological data products, as well as their uncertainties, are in development but not yet part of the operational workflow. All of these functions are located within the data.atmosphere module.

Once data is in the standard format and processed, it will be converted to the model-specific format using a met2model.MODEL function (located in that MODEL’s module).

More detailed information on how PEcAn processes inputs can be found on our [Input Conversion] page.

6.2.3 Troubleshooting meteorological conversions

At the current moment, most of the issues below address possible errors that the Ameriflux meteorology workflow might report Could not do gapfill … The following variables have NA’s

This error message means that there were gaps in the downloaded data, for whatever variables that were listed, which were larger than the current algorithm could fill. Particularly common is missing radiation or PAR data, as Ameriflux frequently converts nighttime data to NULL, and work is in progress to detect this based on solar geometry. Also common are incomplete years (first or last year of tower operations). Could not get information about . Is this an Ameriflux site?

This message occurs when PEcAn believes that a site is part of Ameriflux (because it was listed on the Ameriflux or FLUXNET webpage and has a US-* site code), but no data is present on the Ameriflux server. The most common reasons for this is that you have selected a site that has not submitted data to Ameriflux yet (or that data hasn’t been processed yet), or you have selected a year that’s outside the tower’s operational period. Visit Ameriflux and FLUXNET for lists of available site years. Could not download data for for the year

This is similar to the previous error, but in this case PEcAn did find data for the site listed, but just not for the year requested. This can usually be fixed by just altering the years of the run to match those with available data. I could not find the requested var (or dimvar) in the file!

PEcAn could not find a required variable within the downloaded file. Most likely this is due to that variable not being measured at this site. The most common cause of failure is the absence of atmospheric pressure data (PRESS), but since most models have a low sensitivity to this variable we are working on methods to estimate this from other sources.