p-TOMCAT: Contributed software (unsupported)

On this page you will find various programs and model updates related to p-TOMCAT. Please note that this software is NOT part of the main model code and as such is unsupported by Glenn and Nick but may be supported by the author (if that person is still around).

Note that the jobs are provided as-is. They will have been tested to work as their author intended but no guarantee is made that they are bug free. They are provided in order to save work re-inventing the wheel!

Binary files

There are 3 types of binary files used and produced by p-TOMCAT; initial files, restart files and PDG files. The format of these files is very similar. Restart files and initial files have the same header. Restart files include the tracer and their first and second order moments, initial files just have the species (not tracer) concentrations. PDG files are the same as initial files but may include additional meteorological fields from the analyses. The programs below that work on these files tend to be very similar and can often be adapted to work with one of the other formats.

PDG / netCDF files

Before p-TOMCAT, the usual model output was in a binary fortran file called a 'PDG' file. You will find code here to manipulate these files. However, with p-TOMCAT the preferred method of outputting model results is to netCDF. PDG files are still useful to output if you want to make exact comparisons between different runs as netCDF results are rounded down to single precision.

Author(s) Program description Download
Apostolos Voulgarakis Reads a restart file and adds an extra field to be used with radon run. Note this not needed for version 2+ of tomcat which can include radon without modifying the restart file. addradon2.f90
Nick Savage Reads a monthly mean single precision file (previously built from PDG output) and uses it to compute the lifetime of methane during that month. tauch4.f
Nick Savage redate3: Flexible program for changing date of PDG and restart files. Handles any number of input or output levels for the meteorology. redate3.zip
Nick Savage dateread: simple Unix script which runs a short program to print out the date string in a TOMCAT initial file, restart file or PDG file. Usage: dateread p-TOMCAT.RESTART dateread
Nick Savage datecode: similar to dateread but returns an 8 figure code yymmddhh which is useful for creating new filenames for physical restart files. datecode
Marcus Koehler pdg2nc: takes TOMCAT PDG files and converts them to netCDF. Useful for older TOMCAT model output (TOMCAT G). pdg2nc.job
Glenn Carver changeres: reads a PDG file and changes the horizontal resolution to give a p-TOMCAT initial file. Tar file includes source code and Makefile. changeres.tar.gz
Glenn Carver vampir.up: Nupdate deck to add Vampir tracing calls to p-TOMCAT v1.1 vampir.up
James Levine time_reorder: reads trajectory output from p-TOMCAT and reorders it as the model does not always output with time increasing because of the parallel nature of the model time_reorder.f90
Nick Savage calc_sm: Calculates box masses and interface pressures from box centre pressures and lattitude interfaces. calc_sm.f90
Glenn Carver coloured_vectors.jnl. Ferret journal script for producing plots of vectors coloured by another variable. colour_vectors.jnl
(see example)
Nick Savage grib2nc: Takes a list of input GRIB files, regrids to T21 and outputs to netcdf. Uses xconv/convsh to do the conversion (see http://www.met.reading.ac.uk/~jeff/xconv/index.html) grib2nc
Glenn Carver convert2height: Ferret script to convert p-TOMCAT netcdf field to height coordinates instead of sigma levels. Requires pressure to be in netcdf output file. convert2height.jnl
Peter Cook peter.tar.gz: Collection of basic IDL procedures and one fortran program to read a netcdf file and print variables names, attributes and basic plots. Note that the ncdump command also provides much the same thing but if you want to write IDL procedures yourself these will help you get started. I'd also recommend looking at GrADS or Ferret to discover variables names and plotting as often it's easier to use these rather than IDL. peter.tar.gz
Glenn Carver xsection.up: nupdate changes to turn TOMCAT into a 'cross-section' model where chemistry is done at all lats & hts but for a single longitude. Bit like a multiple box model, useful for testing rate changes and ASAD code changes. Runs much faster than full model. xsection.up