Pbleonard/GFlow: GFlow: for circuit theory-based connectivity

Software for modeling circuit theory-based connectivity at any scale. We developed GFlow to solve large ecological problems in a High Performance Computing environment. If solving a small problem or if you are willing to sacrifice some performance, it can be deployed on a desktop computer.

v. 0.1.6 Updates

Added two flags for naming output pairs:

1. output_density_filename defines the output current density for every iteration
2. output_sum_density_filename defines the output of the final summed current density

Other changes:

The format of the output is decided by the filename extension. Options are: .asc, .asc.gz, and .amp. Omitting output_density_filename from your command-line options means the solution will be discarded after each iterations. Likewise, if you omit output_sum_density_filename, the final summed current density will be discarded. There are no defaults for these options.

These new options alleviate the need for older flags: output_directory, output_prefix, output_format and output_final_current_only: See execute_example.sh for clarity

• Note: If having difficulty assigning arguments to flags, please check for the most recent description in execute_example.sh on the main repo as this is actively being edited for clarity or specifically for v.0.1.6 see here: https://github.com/Pbleonard/GFlow/issues/8

v. 0.1.5 Updates

Bug fixes. Installation for Linux using PETSc >= 3.7.3. Also included are smaller example inputs for folks testing on desktop computers.

v. 0.1.4 Updates

GFlow will automatically ignore node pairs with that create short circuits (islands). Updated instructions for installation and execution. Bug fixes.

v. 0.1.3 Updates Added options for printing progress of simulation and for cleanly exiting simulation. Documented optional execution flags. Updated input files.

v. 0.1.2 Updates Updated new flags for effective resistance (effective_resistance), convergence factor (converge_at), and shuffle node pairs (shuffle_node_pairs)