Multiple recruitment time series turning up in different boxes
A new flagrecruit option has been added to both the bec_dev Atlantis2 branch as well as AtlantisDem. If you set flagrecruit to 18 you can now enter different recruitment time series into each box (or as many boxes as you like). This same code is triggered if flagstockingXX is set to 1 for group XX.
In addition you will need to add some information to your force.prm
nMultRects n
typeMultRects i
where n is the number of time series and i is either 0 if interpolating between values in the time series or 1 if just using the last value in the time series compared to the time in the model when the time series is called
then for each individual time series you need to put in the following
MultRectsK.name name_for_your_reference
MultRectsK.location x y b
MultRectsK.data file_pathway
MultRectsK.rewind j
where
K is the number of the time series (0 to n-1 if you have n time series)
name_for_your_reference is a string (no spaces) that describes the timeseries for the modellers reference (not actually used within Atlantis itself)
x is the x coordinate of a point inside the destination
box
y is the y coordinate of a point inside the destination box
b is the id of the destination box (seems a bit redundant when you give x and y I know, but its so we can cross reference and double check it goes in the correct spot)
file_pathway is the path and filename of the actual time series file
j is either 0 if you use the time series once until it runs out or 1 if you want it to rewind and start again if you reach the end of the file before the run is complete
A worked example of what needs to go into the force.prm
Here is an example for 2 time series, you can have up to as many time series as you have boxes
Forced recruitment lists, when coming in multiple locations simultaneously
nCatchts is the number of time series to be loaded and
typeCatchts is whether or not the data is to be interpolated (0) by the model
or just use previous record (1)
nMultRects n
typeMultRects 1
MultRects0.name box1ts
MultRects0.location 1848738.108 2182817.837 1
MultRects0.data inputs/larval/larval1.ts
MultRects0.rewind 0
MultRects1.name box2ts
MultRects1.location 2461585.926 2395123.978 2
MultRects1.data inputs/larval/larval2.ts
MultRects1.rewind 0
Format of the ts file itself
As with the catch.ts files you must put in a column for each age structured functional group in the model (you can put in columns for the other groups too if you want but of no actual use) with the contents of the column the number of new recruits being added at that location at that time (it is safest just to add the total number of recruits as spawning happens in “once per go” rather than continuously in Atlantis). If a group is using a different flagrecruit than 18 for a group just fill that column with zeros as it won’t be used anyway. Sorry about having such a big blank entry requirement but it is easiest to implement with least chance for error.
The format of the header file is best expressed with an example (with one row of data included at the end):
Example larval file until 2000 for box 2
COLUMNS 51
COLUMN1.name Time
COLUMN1.long_name Time
COLUMN1.units days since 1910-01-01 00:00:00 +10
COLUMN1.missing_value 0
COLUMN2.name FPL
COLUMN2.long_name FPL
COLUMN2.units number
COLUMN2.missing_value 0
COLUMN3.name FPO
COLUMN3.long_name FPO
COLUMN3.units number
COLUMN3.missing_value 0
COLUMN4.name FPS
COLUMN4.long_name FPS
COLUMN4.units number
COLUMN4.missing_value 0
COLUMN5.name FVD
COLUMN5.long_name FVD
COLUMN5.units number
COLUMN5.missing_value 0
COLUMN6.name FVV
COLUMN6.long_name FVV
COLUMN6.units number
COLUMN6.missing_value 0
COLUMN7.name FVS
COLUMN7.long_name FVS
COLUMN7.units number
COLUMN7.missing_value 0
COLUMN8.name FVB
COLUMN8.long_name FVB
COLUMN8.units number
COLUMN8.missing_value 0
COLUMN9.name FVT
COLUMN9.long_name FVT
COLUMN9.units number
COLUMN9.missing_value 0
COLUMN10.name FVO
COLUMN10.long_name FVO
COLUMN10.units number
COLUMN10.missing_value 0
COLUMN11.name FMM
COLUMN11.long_name FMM
COLUMN11.units number
COLUMN11.missing_value 0
COLUMN12.name FMN
COLUMN12.long_name FMN
COLUMN12.units number
COLUMN12.missing_value 0
COLUMN13.name FBP
COLUMN13.long_name FBP
COLUMN13.units number
COLUMN13.missing_value 0
COLUMN14.name FDD
COLUMN14.long_name FDD
COLUMN14.units number
COLUMN14.missing_value 0
COLUMN15.name FDE
COLUMN15.long_name FDE
COLUMN15.units number
COLUMN15.missing_value 0
COLUMN16.name FDS
COLUMN16.long_name FDS
COLUMN16.units number
COLUMN16.missing_value 0
COLUMN17.name FDM
COLUMN17.long_name FDM
COLUMN17.units number
COLUMN17.missing_value 0
COLUMN18.name FDP
COLUMN18.long_name FDP
COLUMN18.units number
COLUMN18.missing_value 0
COLUMN19.name FDB
COLUMN19.long_name FDB
COLUMN19.units number
COLUMN19.missing_value 0
COLUMN20.name FDC
COLUMN20.long_name FDC
COLUMN20.units number
COLUMN20.missing_value 0
COLUMN21.name FDO
COLUMN21.long_name FDO
COLUMN21.units number
COLUMN21.missing_value 0
COLUMN22.name FDF
COLUMN22.long_name FDF
COLUMN22.units number
COLUMN22.missing_value 0
COLUMN23.name SHB
COLUMN23.long_name SHB
COLUMN23.units number
COLUMN23.missing_value 0
COLUMN24.name SHD
COLUMN24.long_name SHD
COLUMN24.units number
COLUMN24.missing_value 0
COLUMN25.name SHC
COLUMN25.long_name SHC
COLUMN25.units number
COLUMN25.missing_value 0
COLUMN26.name SHP
COLUMN26.long_name SHP
COLUMN26.units number
COLUMN26.missing_value 0
COLUMN27.name SHR
COLUMN27.long_name SHR
COLUMN27.units number
COLUMN27.missing_value 0
COLUMN28.name SSK
COLUMN28.long_name SSK
COLUMN28.units number
COLUMN28.missing_value 0
COLUMN29.name SB
COLUMN29.long_name SB
COLUMN29.units number
COLUMN29.missing_value 0
COLUMN30.name SP
COLUMN30.long_name SP
COLUMN30.units number
COLUMN30.missing_value 0
COLUMN31.name PIN
COLUMN31.long_name PIN
COLUMN31.units number
COLUMN31.missing_value 0
COLUMN32.name REP
COLUMN32.long_name REP
COLUMN32.units number
COLUMN32.missing_value 0
COLUMN33.name WHB
COLUMN33.long_name WHB
COLUMN33.units number
COLUMN33.missing_value 0
COLUMN34.name WHS
COLUMN34.long_name WHS
COLUMN34.units number
COLUMN34.missing_value 0
COLUMN35.name WHT
COLUMN35.long_name WHT
COLUMN35.units number
COLUMN35.missing_value 0
COLUMN36.name WDG
COLUMN36.long_name WDG
COLUMN36.units number
COLUMN36.missing_value 0
COLUMN37.name CEP
COLUMN37.long_name CEP
COLUMN37.units number
COLUMN37.missing_value 0
COLUMN38.name BFS
COLUMN38.long_name BFS
COLUMN38.units number
COLUMN38.missing_value 0
COLUMN39.name BFF
COLUMN39.long_name BFF
COLUMN39.units number
COLUMN39.missing_value 0
COLUMN40.name BFD
COLUMN40.long_name BFD
COLUMN40.units number
COLUMN40.missing_value 0
COLUMN41.name BG
COLUMN41.long_name BG
COLUMN41.units number
COLUMN41.missing_value 0
COLUMN42.name BMD
COLUMN42.long_name BMD
COLUMN42.units number
COLUMN42.missing_value 0
COLUMN43.name BML
COLUMN43.long_name BML
COLUMN43.units number
COLUMN43.missing_value 0
COLUMN44.name BMS
COLUMN44.long_name BMS
COLUMN44.units number
COLUMN44.missing_value 0
COLUMN45.name PWN
COLUMN45.long_name PWN
COLUMN45.units number
COLUMN45.missing_value 0
COLUMN46.name ZL
COLUMN46.long_name ZL
COLUMN46.units number
COLUMN46.missing_value 0
COLUMN47.name BD
COLUMN47.long_name BD
COLUMN47.units number
COLUMN47.missing_value 0
COLUMN48.name MA
COLUMN48.long_name MA
COLUMN48.units number
COLUMN48.missing_value 0
COLUMN49.name FPM
COLUMN49.long_name FPM
COLUMN49.units number
COLUMN49.missing_value 0
COLUMN50.name FPA
COLUMN50.long_name FPA
COLUMN50.units number
COLUMN50.missing_value 0
COLUMN51.name SBP
COLUMN51.long_name SBP
COLUMN51.units number
COLUMN51.missing_value 0
0 0.00E+00 1.22E+00 0.00E+00 0.00E+00 5.08E-01 2.21E+01 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 3.55E+01 0.00E+00 4.57E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 5.08E-01 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 1.52E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 7.53E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00