Command Line Interface

serpentTools includes minor command line functionality. Provided you have installed according to Installation, you can access this interface with:

$ serpentTools

where the above command is executed from the terminal, neglecting the $. More information can be found in Terminal terminology.

Display the available options by passing the -h flag:

$ serpentTools -h
usage: serpentTools [-h] [--version] [-v | -q] [-c CONFIG_FILE]
                    {seed,list,to-matlab} ...

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -v                    increase verbosity v: info, vv: debug
  -q                    suppress warnings and errors q: error, qq: critical
  -c CONFIG_FILE, --config-file CONFIG_FILE
                        path to settings file

                        sub-command help
    seed                copy an input file with unique random number seeds
    list                show the default settings
    to-matlab           convert output file to .mat file

Random Seed Generation

The seed subcommand utilizes the serpentTools.seed module to produced repeated input files with unique random seeds This is helpful for running repeated analyses to reduce the stochastic nature of Monte Carlo calculations. Options for forcing the number of digits, utilizing the SERPENT include command rather than fully copying the file, and new output directories are afforded to the user.

$ serpentTools seed -h
usage: serpentTools seed [-h] [--seed SEED] [-l LENGTH]
                         [--output-dir OUTPUT_DIR] [--link]
                         file N

positional arguments:
  file                  input file to copy
  N                     integer number of files to create

optional arguments:
  -h, --help            show this help message and exit
  --seed SEED           Seed to start with the builtin random generator
  -l LENGTH, --length LENGTH
                        Number of digits in random seeds
  --output-dir OUTPUT_DIR
                        Copy files into this directory
  --link                Reference input file with include statement, rather
                        than copying the whole file

Conversion to Binary .mat files

Starting in version 0.6.2, serpentTools can convert text SERPENT output files and convert them to binary .mat files. This relies upon scipy, and can be called from the command line as follows:

$ serpentTools to-matlab -h
usage: serpentTools to-matlab [-h] [-o OUTPUT] [-a] [--format {4,5}] [-l]
                              [--large] [--oned {col,row}]

positional arguments:
  file                  output file to read and convert

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Name of output file to write. If not given, replace
                        extension with .mat
  -a, --append          Append to existing file if found. Otherwise overwrite.
                        Default: False
  --format {4,5}        Format of file to write. 4 for MATLAB 4, 5 for MATLAB
                        5+. Default: 5
  -l, --longNames       Allow variable names up to 63 characters. Otherwise,
                        enforce 31 character names. Default: False
  --large               Don't compress arrays when writing.
  --oned {col,row}      Write 1D arrays are row or column vectors

Conversion will exit with no errors if the file is able to be converted, or with the following exit codes:

  • 1: scipy not found

  • 3: That file type is not supported at this time.

If you desperately need a file type to be converted, please reach out to the developers on the GH Issue board. Alternatively, if you’re feeling ambitious, follow through the Developer’s Guide for guidelines on adding the feature and submitting a pull request.