# Files contained in this directory.
| File                          | Description                                                    |
|-------------------------------|----------------------------------------------------------------|
| aoi-2009                      | Passive particle tracking for 2009.                            |
| aoi-2011-2-min-timestep       | Particle tracking for 2009 using a 2 minute timestep.          |
| aoi-2011-fixed-depth          | Fixed-depth particle tracking for 2011.                        |
| aoi-2011-fixed-depth-hourly   | Fixed-depth particle tracking for 2011 with hourly releases.   |
| aoi-2011-no-fixed-depth       | Passive particle tracking for 2011 with daily releases.        |

# Files contained in the subdirectories aoi-* (alphabetical order).
| File                             | Description |
| -------------------------------- | ----------- |
| fiscm                            | A symbolic link to the FISCM binary. |
| fiscm\_group\_001.nc             | The particle-tracking output from FISCM. |
| initial\_xyz.txt                 | The initial x, y, z, and t locations for the particles. |
| lcs                              | The Lagrangian coherent structures tracking and results in directories numbered according to R's numeric representation of the release date. |
| postproc                         | A symbolic link to the postprocessing binary. |
| qsub-{pld-min}.sh                | A qsub file for running the postprocessing with the run control for a PLD minimum length of {pld-min} days. The qsub files should all be checked before use, there are other segments commented out when runs finish partway through. |
| qsub_fiscm.sh                    | A qsub file for running FISCM. |
| run.nml                          | The run configuration for FISCM. |
| run\_pp\_{radius}\_{pld-min}.nml | The run configuration for postprocessing with a settlement radius of {radius} meters and minimum PLD length of {pld-min} days. |
| settlers\_{radius}\_{pld-min}.nc | The postprocessing output for postprocessing with a settlement radius of {radius} meters and minimum PLD length of {pld-min} days. |

# Postprocessing file format
| Variable           | Description |
| ------------------ | ----------- |
| time               | The time dimension.            |
| travel\_time       | The age of the particle at settlement in days. |
| travel\_dist       | The cumulative distance traveled by the particle at the time of settlement. |
| start\_island      | An integer between 1 and 14 corresponding to the starting AOI number. |
| end\_island        | An integer between 1 and 14 corresponding to the destination AOI number. |
| drift\_start\_time | The time of particle release (days since 2010-10-01). |
| stuck              | Is the particle stuck? This is the same as the FISCM variable of the same name. |
| x                  | The x position of the particle. |
| y                  | The y position of the particle. |
| z                  | The depth of the particle. |
| pathlength         | The cumulative distance traveled by the particle (m). |
| id                 | The index of this particle into fiscm\_group\_001.nc. |