FATES History Outputs

Concatonating history files

By default FATES will output monthly files, containing values that are the average value for that month. To visualize the simulation we want to read a single file into Python or R, with all the months combined. To do this we use the NCO tool ncrcat.

ncrcat -h fates_tag.elm.h0.*.nc  fates_tag.sofar.nc

The -h flag tells ncrcat not to copy meta data from the input files to the new file. The * tells ncrcat to combine all files that have elm.h0. in the name, regardless of the date. fates_tag should be replaced by the full name of your FATES simulation. The new file ending .sofar.nc contains the full time series of the model run and can be loaded into R or Python to make figures.

To see examples of R and Python scripts that plot FATES outputs go to the Jupyter book lesson 3.

Changing the output frequency

By default FATES produces monthly files that record the state of the forest. These are saved in the output directory as elm.h0. files. To change the frequency that the files are written out, or the resolution of the outputs we can change two arguments in the user_nl_elm file by editing our create script. The frequency of the history file streams is given by the namelist variable hist_nhtfrq. The values of hist_nhtfrq must be integers, where the following values have the given meaning: Positive value means the output frequency is the number of model steps between output. Negative value means the output frequency is the absolute value in hours given (i.e -1 would mean an hour and -24 would mean a full day). Zero means the output frequency is monthly. The number of samples on each history file stream is given by the namelist variable hist_mfilt. Examples are given in the table below.

File frequency	Time stamp	hist_nhtfrq	hist_mfilt	Description
Annual	Annual	-8760	1	Annual outputs written out yearly
Annual	Monthly	0	12	Monthly outputs written out yearly
Annual	Daily	-24	365	Daily outputs written out yearly
Annual	Hourly	-1	8760	Hourly outputs written out yearly
Monthly	Monthly	0	1	DEFAULT Monthly outputs written out monthly
Daily	Daily	-24	1	Daily outputs written out daily
Daily	Hourly	-1	24	Daily outputs written out hourly
Hourly	Hourly	-1	1	Hourly outputs written out hourly
Five years	Monthly	0	60	Monthly outputs written out every five years
Ten years	Annual	-8760	10	Annual outputs written out every ten years

FATES history dimensions

The history writing code in FATES is contained in this file: main/FatesHistoryInterfaceMod.F90

FATES history variables can be output along different dimensions. For example, FATES_LAI is output at the site level, meaning we have a single value per month of the simulation representing the mean LAI of each month, over the whole site where we are running FATES. In a regional or global run, we would have one value per month per grid cell.

Other dimensions are indicated by the ending of the variable name.

_suffix	Dimension
_PF	site x pft
_SZ	site x size
_SZPF	site x size x pft
_AP	site x patch age
_FC	site x fuel class
_SL	site x soil
_APFC	site x patch age x fuel class
_EL	site x element (e.g. Carbon, Nitrogen or Phosphorus)
_CLLL	site x canopy layer x leaf layer
_SZAP	site x size x patch age
_SZAPPF	site x size x patch age x pft
_APPF	site x patch age x pft
_DC	site x coarse woody debris class

At the end of the FatesHistoryInterfaceMod.F90 script is a list of all the FATES history ouptuts. An example output looks like this:

call this%set_history_var(vname='FATES_LEAFMAINTAR',                       &
            units = 'kg m-2 s-1',                                                &
            long='leaf maintenance autotrophic respiration in kg carbon per m2 per second', &
            use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM',    &
            upfreq=group_hifr_simple, ivar=ivar, initialize=initialize_variables,                &
            index = ih_leaf_mr_si)

vname is the variable name that you will use in any post processing. units tells us what units the output has. long is a description of the variable. use_default tells us if the variable is output by default ‘active’ or if we would need to specify it in the user_nl_elm part of the create script. vtype tells us what dimension the variable has - here just site.