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NOAA-EDAB / atlantisdrive

https://noaa-edab.github.io/atlantisdrive/
https://noaa-edab.github.io/atlantisdrive/
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atlantisdrive

deploy to github pages Install on windows gitleaks

Tools for moving Atlantis files to and from Google drive

Installation

remotes::install_github("NOAA-EDAB/atlantisdrive")

Usage

To run Atlantis the command takes on the form like:

atlantisMerged -i neus_init.nc 0 -o neus_output.nc -r at_run.prm -f at_force_LINUX.prm 
-p at_physics.prm -b at_biology.prm -h at_harvest.prm -e at_economics.prm -s neus_groups.csv
-q neus_fisheries.csv -t . -d output

where neus_output.nc is the main output file. The prefix neus_output is prepended to all Atlantis output files.

library(atlantisdrive)

To view the list of files/folders under the root folder (as defined by id) on Google drive use

get_file_list()
get_file_list(targetDir = "Development")
get_file_list(targetDir = "Development/Example")

To pull all files containing the string “ATLNT” from the “Development” folder to your local machine (Note: partial matches to file names are allowed)

pull_from_drive(localPath=here::here(),fileList="ATLNT",googledriveFolder="Development")

To push all files from your “output” folder in your current working directory to the “Testing/Example” folder on Google drive (Note: partial matches to file names are allowed). All files are overwritten.

push_to_drive(id=NULL, localPath=here::here("output"), fileList=NULL, googledriveFolder="Testing/Example", rootid=atlantisdrive::rootid, overwrite = TRUE)

Note: special case when fileList = NULL. All Atlantis core files are pushed.

To push all files containing the string “xml” from your “output” folder in your current working directory to the “Testing/Example” folder on Google drive. Appends the string “climate” to beginning of all files

push_to_drive(id="climate", localPath=here::here("output"), fileList="xml", googledriveFolder="Testing/Example", rootid=atlantisdrive::rootid, overwrite = TRUE)

Contact

andybeet

Contributors (alphabetical order)

jcaracappa1 sgaichas gambler1650 slarge

Legal disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.