Spatially-varying diagnostic quantities

Sometimes it is useful to have PISM save a handful of diagnostic maps at some interval, for example every 10 years or even every month. One can use snapshots (section Snapshots of the model state), but doing so can easily fill your hard-drive because snapshots are complete (i.e. re-startable) model states. Sometimes you want a subset of model variables saved frequently.

Use options -extra_file, -extra_times, and -extra_vars for this. For example,

pismr -i foo.nc -y 10000 -o output.nc \
      -extra_file extras.nc \
      -extra_times 0:10:1e4 \
      -extra_vars velsurf_mag,velbase_mag

will run for \(10000\) years, saving the magnitude of horizontal velocities at the ice surface and at the base of ice every 10 years. Times are specified using a comma-separated list or a MATLAB-style range. See Parameters below for all the parameters controlling this feature. The section Spatially-variable fields list all the variable choices.

Note

Some diagnostics are only available if the simulation uses a sub-model that provides them. PISM will stop with an error message if a diagnostic is requested but not available. To print a warning and continue instead of stopping, set output­.extra­.stop_missing to “false”.

Note that options -extra_times, -save_times, -ts_times take dates if a non-trivial calendar is selected. Here are some examples.

pismr ... -extra_times 10       # every 10 years
pismr ... -extra_times 2days    # every 2 days
pismr ... -calendar gregorian \
          -extra_times 1-1-1:daily:11-1-1 # daily for 10 years
pismr ... -calendar gregorian \
          -extra_times daily -ys 1-1-1 -ye 11-1-1
pismr ... -calendar gregorian \
          -extra_times 2hours -ys 1-1-1 -ye 1-2-1

The step in the range specification can have the form Nunit, for example 5days. Units based on “months” and “years” are not supported if a non-trivial calendar is selected.

In addition to specifying a constant step in -extra_times a:step:b one can save every hour, day, month, or every year by using hourly, daily, monthly or yearly instead of a number; for example

pismr -i foo.nc -y 100 -o output.nc -extra_file extras.nc \
      -extra_times 0:monthly:100 -extra_vars dHdt

will save the rate of change of the ice thickness every month for 100 years. With -calendar none (the default), “monthly” means “every \(\frac 1 {12}\) of the year”, and “yearly” is “every \(3.14\ldots\times10^7\)” seconds, otherwise PISM uses month lengths computed using the selected calendar.

It is frequently desirable to save diagnostic quantities at regular intervals for the whole duration of the run; options -extra_times, -ts_times, and -save_times provide a shortcut. For example, use -extra_times yearly to save at the end of every year.

This is especially useful when using a climate forcing file to set run duration:

pismr -i foo.nc -surface given -surface_given_file climate.nc \
      -calendar gregorian -time_file climate.nc \
      -extra_times monthly -extra_file ex.nc -extra_vars thk

will save ice thickness at the end of every month while running PISM for the duration of climate forcing data in climate.nc.

Times given using -extra_times describe the reporting intervals by giving the endpoints of these reporting intervals. The save itself occurs at the end of each interval. This implies, for example, that 0:1:10 will produce 10 records at times 1,…,10 and not 11 records.

If the file foo.nc, specified by -extra_file foo.nc, already exists then by default the existing file will be moved to foo.nc~ and the new time series will go into foo.nc. To append the time series onto the end of the existing file, use option -extra_append.

The list of available diagnostic quantities depends on the model setup. For example, a run with only one vertical grid level in the bedrock thermal layer will not be able to save litho_temp, an SIA-only run does not use a basal yield stress model and so will not provide tauc, etc. To see which quantities are available in a particular setup, use the option -list_diagnostics spatial, which prints the list of diagnostics and stops.

The -extra_file mechanism modifies PISM’s adaptive time-stepping scheme so as to step to, and save at, exactly the times requested. By contrast, as noted in subsection Scalar diagnostic quantities, the -ts_file mechanism does not alter PISM’s time-steps and instead uses linear interpolation to save at the requested times in between PISM’s actual time-steps.

Parameters

Prefix: output.extra.

  1. append (no) Append to an existing output file. No effect if file does not yet exist, and no effect if output­.extra­.split is set.

  2. file Name of the file that will contain spatially-variable diagnostics. Should be different from output­.file.

  3. split (no) Save spatially-variable diagnostics to separate files (one per time record).

  4. stop_missing (yes) Stop if requested variable is not available instead of warning.

  5. times List or a range of times defining reporting intervals for spatially-variable diagnostics.

  6. vars Comma-separated list of spatially-variable diagnostics.

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