Atlantis Ecosystem Model
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R code to process ROMS into Hydro
Getting Started
Atlantis Ecosystem Model Wiki
Atlantis Ecosystem Model Home Page
New User Atlantis Workflow
Atlantis FAQ
Getting Help
Documentation
Atlantis Documentation
Further detail on Atlantis components
Biology Equations
BioPhysics Equations
Building & Running
Building Atlantis
Running Atlantis
How to run
Parameters & Input Files
Atlantis Parameter Files
Functional Group Definition File
Initial Conditions NetCDF File
Forcing Files
Updates & Changes
Atlantis Changelog
All Pages
ratlantis: an R package for interfacing with Atlantis ecosystem modeling software
How to handle “unrecognized command line option”
Summit Presentations & Photos
Modifying & Extending Atlantis
SVN & Using Code Repository
Models & Scenarios - SVN
2015 Summit
2022 Summit
Stock Recruit parameters (Beverton Holt)
R code, add climate trends to Hydro.NC
Q&A
Atlantis_TODO - Bec’s task list
Debian (or other Debian-based distributions, e.g. Ubuntu)
Debug (fprintf calibration) options
So, you’re thinking of building an Atlantis model…
External Mortality, Growth and Recruitment Scaling
Change executable name under linux/mac
Bec, Mike and Brian 3rd Jul 2008
Set-up - Software & Code
Updating the input files were JCEP and JPWN were ‘separate’ groups
Using CSIRO High Performance Comping (HPC) for Atlantis
Add a input parameter
Add in Wind - helper notes
Adding a new group
Adding a new GroupType
All
AMS-Climate Model
AMS - SE Atlantis Model
Antarctic Model Geometry
Antarctica
Applications
Asking for help with your Atlantis model
Atlantis_Tags
Atlantis BGM Files
Atlantis California Current Model Review
Atlantis Documentation
Atlantis Ecosystem Model Home Page
Atlantis FAQ
Atlantis Google Group
Atlantis Helper Tools
Atlantis in Parallel
Atlantis NetCDF Structure
Atlantis on Mavericks with Homebrew
Atlantis Output Files
Atlantis Parameter Files
Atlantis Summit
Atlantis Training Laptop Setup
AtlantisGroupTypes
AtlantisNCGen
atLink
atLink Module
Availability Calculator
Bec and Brian 2nd Jul 2008
BGM and Atlantis model shapefiles
BGM Editor Redevelopment
BGM Mapper
BGM2SHP
BGMEditor
Biology Equations
Biology input file
BiomIndx.txt
BioPhysics Equations
BrokenStick
BrokerLink
Building Atlantis
Building Atlantis on a CSIRO Bowen Machine
Building Atlantis using an older version of gcc
Building on a 64-bit machine
Building under CentOS
Building under cygwin
Building under linux
Building under mac
Building under windows
Building using docker
California-Current ECCAL
CatchPerFishery.txt
CDFDistiller
Change Log
Changed to Initial Conditions NetCDF file
Changed to prm files
Atlantis Changelog
Checkwinding
Climate Change
Code changes that effect model output.
Code Documentation
Common Windows Build Errors
Compile on Windows using MinGW
Conceptual Models
Connect to Bowen Storage
Contaminant Modelling
Contaminants in Atlantis
Creating your own personal configure script
CSIRO Bowen Research Cloud
CSIRO licence and repository request
Current Coverage Results
Current Forcing File Structure
Developers Area
DietCheck.txt
Differences in Output
Differences in Windows and Linux
Discussion Groups
Donut Diet Model
Effect of temperature on functional groups
Error Message library
EwE Climate Workshop
Excel diet spreadsheet for Atlantis Diets
Existing Atlantis Bowen Capacity
Fedora
File Formats
Finding all the options for the flags
Fisheries flag options
Fisheries Input File
Fisheries.xml
Fishery Definition File
Fishing
Force Input File
Forcing Files
FriendShip Network
Functional Group Definition File
Further detail on Atlantis components
Future functionality
Get a particular code revision
Getting Help
Getting the source code
Greater climate effects control
groupAgeType
GUI for config files
Habitat Parameters
Handy Excel Spreadsheets
HC - Building in Linux and Mac
HC - Building in Windows
Hobart Atlantis user group
How-to articles
How to run
How to view
Hydro FAQ
Hydro files - format description
HydroConstruct
Ice Forcing files
Ice groups
Ice in Atlantis
Icelandic model. Vertebrate not reproducing.
Initial Conditions Errors
Initial Conditions NetCDF File
Input Files Changes
Installing and using NCO on windows
Interaction with atecology
JRE model. Unstable tracer NH3
Land in Atlantis
Larval Dispersion
Learn now to navigate the Linux Terminal
Lecture Material
Linking Models
MacroEcology Discussions
Matlab - Hydro
Migration to the new Atlantis code
Mini Development Initial Notes
MINI2 - Atlantis Configuration GUI
Miscellaneous Parameter_Notes
Model Components
Model Redevelopment
Mortality Output files
NetCDF 4 in Windows
NetCDF library -Old 3.6.1
New User Atlantis Workflow
oa-16-mel.it.csiro.au
oa-22-mel.it.csiro.au
Octave
Open connection to Bowen Compute
Output Splitter
Parameterising Atlantis
Parameterising initial abundance and distribution
Physics Input File
Profiles for different levels of user
Python script to extract biomass data from the log file
R code for plotting spatial biomass
R-code spatial analysis AtlantisNEUS
R code to process ROMS into Hydro
R Notes
R Script to duplicate group values in prm file
Rain and Evaporation
Recruitment forcing
Recruitment Options
Related Projects
rlantis
Run Input File
runAtlantisInterface
Running Atlantis
Running Atlantis on the Bowen
Running Hydroconstruct
Salish Sea
Salish Sea Oil Spill Modelling
Sample input files
Scaling point sources
Seap 4000 day results
Session Notes
Setting up an EwEService instance
Software Engineering Practices
Solar Radiation
Start a VNCServer instance on cluster machines
Stepping through model issues by looking through the Atlantis code.
Storm Bay
Summit Participants
Switch working copy to another branch
tasCERF
TasCERF Atlantis Model
Technical Information
Temperature and Salinity File Structure
TortoiseCVS
TortoiseSVN
Ubuntu
Updating Visual Studio include and library folders
Upgrading to new Visual Studio Version
Useful Code
Useful Linux Commands
Useful Mappings
Useful Reading
Useful shortcuts when using netCDF
Useful Tools and Tips
Using Geotools with boxmodels
Using QGIS to clean Atlantis BGM Shapefiles
Using the Intel Compiler
VicMPA
VicMPA 7300 day results
What to do if a compiler setting is causing a compile error
Windows Command Prompt
Writing new functionality in Atlantis
Yearly income set to zero after 365 days
Posts
A useful poster on Atlantis processes in the Chesapeake Bay model (by Tom Ihde and others)
Acidification induced mortality
Added max_available_habitat value to biology file.
Added new option for using fishing mortality and selectivity
Adding continues
Adding noise (error) to biomass estimate used with the Broken Stick Management option
Allowing for more sensitive habitat dependency
Annual biology
Aquaculture
Atlantis and EwE coupling
Atlantis Future Vision
Atlantis memory
Atlantis SVN Repository is ready for use!
Atlantis VS VPN
Atmosphere-sea flux of gases
Atmosphere-sea fluxes of nutrients and gases
Basket Quotas
BGgrazeSed
Biology File - minDepth
Biology - New Temperature correction algorithm
Biology Parameter - UseHardFeedingWindow
Biology XML
Branching cvs repository
Calculation of rugosity related habitat refuge
Calling R from Atlantis - Stock Assessment and TAC setting
Canada DLL issues
Change to prescribed movement - flexible number of time periods per year.
Changed Handling of Reproduction Parameters
Changes made to forcing input file to allow for multiple temperature and salinity files
Changes to assessment input file
Changes to biology and physics to allow sediment light attenuation
Changes to harvest and economics input file
Changes to physics input file to support different scaling per point source
Changes to the MFC code - flag_useOldMFC
Changing growth rates and FSPB over time
Check for PRM Duplicates
Climate in the biology file
Companion Species and linked TACs
Controlling time series relative time stamp - ts_on_hydro_time
CSoap talking to .NET webservice
Daylight
Discard TAC
Eating code.
Ecological Process Changes
End age for the application of fishing mortality
EPI Tracers
EwE Integration
Expanded habitat depndency
Extra parameters
Finishing the jCEP and jPWN work in biology
Fishing
Flag for age structured overall biomass output txt files
flag_report_water_detritus - Include detritus in water column in reporting.
Force box eddy values using netCDF file
Frame-based fisheries management
Frequency of inputs.ts and export.ts
GeoTools
Getting rid of jCEP
Getting rid of the pred_id values.
Group size scale time series input - non-compulsory change to forcing input file
Guild vs Species Assessments
Habitat dependent movement - flag_move_habdepend
Handling discards dependent on the catch of a species
Handling effects of acidification
Handling Light in Atlantis
harvest control rule
Harvest File
Input file changes
Input files to XML
Inter-species dependency of stock recruitment
Invertebrate size calculations for use in size based selectivity
invertProps
isBioEroder
Jackknife recruitment
jPWN continues
KUP, KLP and KDEP
Mapping fleets in assessments - assess_nf
Marie Savina’s Seagrass Model
Merge jPWN changes
Merging trunk into bec_dev
Migration Upgrade
Min vertebrate reproduction size
More habitat modifications
Mortality scale time series input - non-compulsory change to forcing input file
Moving cvs to svn
Multi year TAC
Multiple growth curves and Evolution
Multiple recruitment time series turning up in different boxes
NetCDF input files
New age specific mortality files
New burn-in day setting and Management parameters
New debug check
New debug flag option included - debug = 24
New economic flag - immed_cost_only
New economics parameter
New Input Folder Argument
New Phosphorus tracking
new seagrass modelling option
Noise and Light Pollution
Number of stocks now in csv file
Ontogenetic diets
Output Folder command line argument
Overwintering & Encystment
Padding out mixing
Passive tracer tracking
Potential Atlantis course
Previous changes made to input files
R code for graphical analyses of vertebrate numbers, mass and length-at-age
Read in forcing data for tracers
Recruit stocking
Reference Points
Relaxing the flux tolerance check for an individual box
Replicating old results in the Trunk code.
Representing salmon and migrating group
Scaling of individual variables in point source files + Assessment
Set start date for fixed MPAs
Shot by shot CPUE generation
Shrinkfat update to feeding
Sorting out addition issues in Eat
Species specific mStarve
Species specific Q10 - biology.prm
Sponge functional group type
Stronger habitat growth restrictions for benthos
Tracking temperature experienced by a group
Transport exchanges updated
Turning off quarterly movement influences
Update to recruitment due to expanded migration code
Update to the way time is handled in Atlantis
Updated Diet Input Matrix
Updated movement options
Use TAC with F (fishing mortality) fishing option
vert properties
Wondering about Turbidity in Atlantis and what turbid_refuge is?
All Pages
R code to process ROMS into Hydro
R code to process ROMS into Hydro
Author
Kaplan Issac