Glossary -------- .. glossary:: benchmark runs Selected validation runs made with each release of the model. These runs can be made using Python code in the :term:`tgcmrun/` directory. benchmarks/ Directory in the model root directory containing shell scripts that call :term:`tgcmrun/` for making benchmark runs, some utility scripts, and a subdirectory postproc/ containing scripts that do post-processing on benchmark results. See :ref:`Benchmark Runs ` for more information. Benchmark results (plots) for version |tgcm_version| are available here: :tgcmweb_url:`Benchmarks Results ` continuation run A continuation run continues from the last output history of the previous run. That history (:ref:`START ` time) must be on the first :ref:`OUTPUT ` file provided by the namelist input file. A continuation run must not specify a :ref:`SOURCE ` file or :ref:`SOURCE_START ` time. See also :ref:`Continuation Run ` diagnostic fields A list of diagnostic fields are available to be saved on secondary history files. See section :ref:`Saving Diagnostic Fields `. datadir Directory containing startup history and data files necessary for running the model. This is specified with the :term:`tgcmdata` shell variable in the :term:`job script`. doc/ Subdirectory under the :term:`modeldir` containing documentation, e.g., the User's Guide, Model Description, Release Notes, etc. ESMF "Earth System Modeling Framework". The ESMF library is used in the electro-dynamo code (pdynamo.F in version |version| or later) for regridding between geographic and geomagnetic grids in an mpi environment. This is open software that can be downloaded at https://www.earthsystemcog.org/projects/esmf/download/ If you build the ESMF library, it should be built with the same compiler with which the model is built. execdir The model execution directory. This is the directory where the model is built and executed. It should be on a large temporary disk, capable of storing model object and module code, netCDF output history files, and other data. When a job script is executed from a working directory, the execdir is created if it does not already exist. During a model run, output history files are written to the execdir. The execdir is set in the :term:`job script`. See also :ref:`Execution Directory ` geomagnetic coordinates The electro-dynamo fields (electric potential, electric field, and ion drift velocities) are calculated on a geomagnetic grid, see :ref:`magnetic coordinates ` Globus `Globus Data Sharing Service `_ for scientific research. The |tgcm_version| benchmark history files and post-processing are available via Globus. See :ref:`benchmark_history_files` for more information. history A model history records the state of the model at a discrete instant in :term:`model time`. One or more histories are stored in netCDF history files. initial run An initial run is started from a history on a :ref:`SOURCE ` file (see also :ref:`SOURCE_START `). Subsequent :term:`continuation runs ` do not provide SOURCE or SOURCE_START, but rather search for the :ref:`START ` time on the first :ref:`OUTPUT ` history file provided in the namelist input, and continue the run from there. job script A csh script in the scripts/ directory which, when executed, will build and execute the model. The user defines a few shell variables in the job script, such as the :term:`modeldir`, and the :term:`namelist input`. See example :download:`job script for Linux desktops <../../scripts/tiegcm-linux.job>`, and :download:`job script for Super computer <../../scripts/tiegcm-ys.job>` See :ref:`jobscript` for more detailed information. model time TIEGCM model time is represented by an integer triplet: day,hour,minute, where day is the julian day of the year, and hour is the ut. The variable for model time on history files is mtime(3,ntimes). For example, a history file may contain 24 hourly histories for day 80: mtime = 80,1,0, 80,2,0, ... 81,0,0. modeldir The model root directory. This directory typically contains subdirectories :term:`src/` (model source code), :term:`scripts/` (utility scripts), :term:`doc/` (documentation), and :term:`benchmarks/`. The modeldir is available via :ref:`download `, and is typically a subdirectory of the model working directory (:term:`workdir`). See also :ref:`Model Directory ` namelist input The model reads user specified parameters from the :ref:`namelist input file ` via f90 standard namelist read. Keyword/Value pairs are read from unit 5, and are validated by the input module (input.F). See also :ref:`job scripts `. netCDF TIEGCM output history files are written in `netCDF `_, a self-describing platform-independent data format written and maintained by the UCAR `Unidata `_ program. output File to receive stdout output from the model. This file will be created if it does not exist, or overwritten if it does exist. resolution The TIEGCM can be run in one of two resolutions: * 5 x 5 deg lat x lon, 2 grid levels per scale height (dz = 0.50) * 2.5 x 2.5 deg lat x lon, 4 grid levels per scale height (dz = 0.25) The resolution is set by the "modelres" shell variable in the TIEGCM :ref:`job script `. See also the section on :ref:`Grid Structure and Resolution `. .. note:: The 2.5-degree resolution model is available in version |version|, but it is not fully validated or supported by the public release. scripts/ Subdirectory under the :term:`modeldir` containing supporting and utility scripts, including job scripts, the default namelist input file, several Make files, etc. src/ Subdirectory under the :term:`modeldir` containing the model source code (\*.F, \*.h files). tgcmrun/ Subdirectory under the :term:`modeldir`. The tgcmrun directory contains Python code to make :term:`benchmark runs` for the current release. The 'tgcmrun' command may be used to interactively submit selected benchmark runs, or tgcmrun can be executed from a shell script using command-line options. There are several run_xxxxx shell scripts there demonstrating how to make benchmark runs. tgcmdata A directory path to start-up and other input data files required for running the model. This should be on a large temporary disk. tgcmdata is a csh variable optionally specified in the :term:`job script`. If not specified, the job script will use the :term:`TGCMDATA` environment variable. See also :ref:`job script shell variables `. env var TGCMDATA A linux environment variable that refers to the :term:`tgcmdata`. This environment variable may be used when referring to data files in the namelist read file, e.g., "GPI_NCFILE = `$TGCMDATA/gpi_xxxxx.nc`". See :ref:`namelist read files `. tgcmproc_f90 Post-processor and visualizer for TIEGCM netCDF history files. Written in f90, and available at the `TIEGCM download site `_ See :ref:`tgcmproc_f90 `. tgcmproc_idl Post-processor and visualizer for TIEGCM netCDF history files. This processor is Written in IDL with a GUI, and is available at the `TIEGCM download site `_ See :ref:`tgcmproc_idl `. utproc Post-processor and visualizer for TIEGCM netCDF history files. This processor reads time-series history files and makes ut vs pressure and ut vs latitude contours. It is written in IDL with a GUI, and is available at the TGCM download site. See :ref:`utproc `. workdir User-created local working directory. This will typically contain the model root directory :term:`modeldir` and related namelist input files, job scripts, stdout files, etc. Because the model source files are critical, this should be on backed-up disk, typically under your home directory. Zp Vertical log pressure coordinate ln(p0/p) of the |modeluc|. This is the "lev" coordinate on the history files. See the chapter on :ref:`Altitude Coordinates the NCAR TIEGCM ` for a detailed explanation of the relationship between Zp and Altitude.