Input Files Changes

Author

Fulton, Beth (Environment, Hobart)

Below is a list of miscellaneous input parameter additions that were made early on in code development. Anyone looking for recent parameter additions should look in the blogs section of the wiki.
14-jan-2010

Fishing input file:

flagfishBD 0 1=fishing of deposit feeders, 0=off 0
flagfishMA 0 1=fishing of macroalgae, 0=off 0

flag_access_thru_wc_BD 0 1=can access deposit feeders through the water column, 0=no 0
flag_access_thru_wc_MA 0 1=can access macroalgae through the water column, 0=no 0

FC_caseZL 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseZG 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBFS 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBFD 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBFF 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBG 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBMS 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBMD 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBML 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseCEP 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_casePWN 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBC 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseBD 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseMB 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseMA 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FC_caseSG 33
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

07-jan-2010

Efficiency Values

There should now be EDR and EDL values for all invertebrates. I was going to default the values to 0 but its too easy to miss that they should be set for some groups. In the AMS model the values should be:

  1. Assimilation efficiency of invertebrate consumers on labile detritus
    EDL_BB 0.5 Assim efficiency of sediment bacteria on labile detritus 0.5
    EDL_BD 0.15 Assim efficiency of deposit feeder on labile detritus 0.002 - 0.3
    EDL_BC 0.0 Assim efficiency of benthic carnivores on labile detritus 0.0 - 0.1
    EDL_BO 0.18 Assim efficiency of meiobenthos on labile detritus 0.002 - 0.3
    EDL_BG 0.2 Assim efficiency of benthic grazer on labile detritus 0.12 - 0.25
    EDL_BMS 0.12 Assim efficiency of shallow macrozoobenthos on labile detritus 0.1 - 0.2
    EDL_BML 0.12 Assim efficiency of megazoobenthos on labile detritus 0.1 - 0.2
    EDL_BMD 0.12 Assim efficiency of deep macrozoobenthos on labile detritus 0.1 - 0.2
    EDL_BFS 0.2 Assim efficiency of shallow filter feeder on labile detritus 0.1 - 0.45
    EDL_BFF 0.2 Assim efficiency of other filter feeder on labile detritus 0.1 - 0.45
    EDL_BFD 0.2 Assim efficiency of deep filter feeder on labile detritus 0.1 - 0.45
    EDL_ZS 0.0 Assim efficiency of microzooplankton on labile detritus 0.0 - 0.2
    EDL_ZM 0.12 Assim efficiency of large zooplankton on labile detritus 0.12 - 0.25
    EDL_ZL 0.0 Assim efficiency of large zooplankton on labile detritus 0.0 - 0.2
    EDL_ZG 0.1 Assim efficiency of getlatinous zooplankton on labile detritus 0.1 - 0.25
    EDL_PB 0.5 Assim efficiency of pelagic bacteria on labile detritus 0.5
    EDL_CEP 0.0 Assim efficiency of cephalopods on labile detritus 0.0 - 0.2
    EDL_PWN 0.0 Assim efficiency of prawns on labile detritus 0.0 - 0.2
    EDL_DF 0.0
    EDL_MA 0.0
    EDL_MB 0.0
    EDL_SG 0.0
    EDL_PL 0.0
    EDL_PS 0.0

  2. Assimilation efficiency of invertebrate consumers on refractory detritus
    EDR_ZS 0.05 Assim efficiency of microzooplankton on refractory detritus 0.001 - 0.1
    EDR_ZM 0.03 Assim efficiency of meso-zooplankton on refractory detritus 0.001 - 0.1
    EDR_ZL 0.02 Assim efficiency of large zooplankton on refractory detritus 0.001 - 0.1
    EDR_ZG 0.02 Assim efficiency of gelatinous zooplank on refractory detritus 0.001 - 0.1
    EDR_PB 0.25 Assim efficiency of pelagic bacteria on refractory detritus 0.25
    EDR_BB 0.25 Assim efficiency of sediemnt bacteria on refractory detritus 0.25
    EDR_BD 0.08 Assim efficiency of deposit feeder on refractory detritus 0.001 - 0.15
    EDR_BO 0.08 Assim efficiency of meiobenth on refractory detritus 0.001 - 0.15
    EDR_BC 0.0 Assim efficiency of carnivorous infauna on refractory detritus 0.0 - 0.1
    EDR_CEP 0.0 Assim efficiency of cephalopods on refractory detritus 0.0 - 0.1
    EDR_PWN 0.0 Assim efficiency of prawns on refractory detritus 0.0 - 0.1
    EDR_BFS 0.0 Assim efficiency of shallow filter feeders on refractory det. 0.0 - 0.1
    EDR_BFD 0.0 Assim efficiency of deep filter feeders on refractory detritus 0.0 - 0.1
    EDR_BFF 0.0 Assim efficiency of other filter feeders on refractory detritus 0.0 - 0.1
    EDR_BML 0.0 Assim efficiency of megazoobenthos on refractory detritus 0.0 - 0.1
    EDR_BMD 0.0 Assim efficiency of deep macrozoobenthos on refractory detritus 0.0 - 0.1
    EDR_BMS 0.0 Assim efficiency of shallow macrozoobenthos on refractory det. 0.0 - 0.1
    EDR_BG 0.0 Assim efficiency of benthic grazers on refractory detritus 0.0 - 0.1
    EDR_DF 0.1
    EDR_MA 0.0
    EDR_MB 0.0
    EDR_SG 0.0
    EDR_PL 0.0
    EDR_PS 0.0

Age structured prey values

#Flag to indicate that the group uses age structured prey.
age_structured_prey_FVD 1
age_structured_prey_FVV 1
age_structured_prey_FVS 1
age_structured_prey_FVB 1
age_structured_prey_FVT 1
age_structured_prey_FVO 1
age_structured_prey_FMM 1
age_structured_prey_FDD 1
age_structured_prey_FDS 1
age_structured_prey_FDB 1
age_structured_prey_FDC 1
age_structured_prey_FDO 1
age_structured_prey_FDE 1
age_structured_prey_FDF 1
age_structured_prey_SHB 1
age_structured_prey_SHD 1
age_structured_prey_SHC 1
age_structured_prey_SHP 1
age_structured_prey_SHR 1
age_structured_prey_FPL 0
age_structured_prey_FPO 0
age_structured_prey_FPS 0

age_structured_prey_FBP 0
age_structured_prey_FMN 0
age_structured_prey_FDM 0
age_structured_prey_FDP 0
age_structured_prey_SSK 0
age_structured_prey_SB 0
age_structured_prey_SP 0
age_structured_prey_PIN 0
age_structured_prey_REP 0
age_structured_prey_WHB 0
age_structured_prey_WHS 0
age_structured_prey_WHT 0
age_structured_prey_WDG 0

15-jun-2009

Efficiency Values

Added efficiency values for invertebrate for Plants.
All consumer invertebrates should have a value. - DF - The DF group was using the E_ value for plants and EDR. The ELD value was over written with 0. - Users need to change the EDR and E_Plant values to the value they were using FLAG_E and set the FLAG_EDL to 0.0. - SED_EP_FF and MOB_EP_OTHER groups were using 0.0 for the EDR value. This value is now rad in from the input file and should be 0.0; - ED_EP_OTHER the E1 value was forced to 0.0, the E_1 value in the input file was used for E_PLANT, and the E4 value was forced to 0.0. The new code uses the values in the input files. So you should change your input files to use the E_BG value for EPLANT_BG, and set the E_BG E_EDR values to 0.0.

16-Jun-2009

init_scalar - I have had to change the init_scaler array in the run file to have num_tot_sp values.

so it was:

  1. Multiplicative scalr for vertebrate initial densities (as read-in from cdf file)
    init_scalar 35
    0.25 1 0.75 1 0.67 1 1 0.8 1 1 1 1 1 1 0.3 1 1 1 1 0.28 1 0.5 0.8 0.2 1 0.3 1.2 1 0.7 1 0.135 1 1 1 1

and it becomes _ the invert values are just padded with 0’s.:

  1. Multiplicative scalr for vertebrate initial densities (as read-in from cdf file)
    init_scalar 62
    0.25 1 0.75 1 0.67 1 1 0.8 1 1 1 1 1 1 0.3 1 1 1 1 0.28 1 0.5 0.8 0.2 1 0.3 1.2 1 0.7 1 0.135 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
06-07-2009

I have had to make some assumptions about the functional group codes.
When the user specifies these using the functional group input file it will assume that they are capitals. This allows me to parse the input files easily.

13-09-2010

The detritus groups must be last in the functional group input file.

The fstat input file has been adjusted slightly.

7-12-2010

min and max depth values.
The old biology input files have the following input values:

  1. Benthic depth stratification markers
    Bmindepth 150 Minimum depth deep benthic groups found at 150
    Bmaxdepth 250 Maximum depth shallow benthic groups fount at 250

Bmindepth is used as the min depth for BFFguild_id, BFDguild_id and BMDguild_id.
BmaxDepth is used as the max depth for BFSguild_id, BMLguild_id and BMSguild_id.

The new code removes these assumptions. If you want the same output you need to use the following:

BFF_mindepth 150
BFD_mindepth 150
BMD_mindepth 150
BFS_mindepth 0
BML_mindepth 0
BMS_mindepth 0

BFS_maxdepth 250
BML_maxdepth 250
BMS_maxdepth 250
BFF_maxdepth 5000
BFD_maxdepth 5000
BMD_maxdepth 5000

24-02-2011

BMDmax 0

07-06-2011

Have created some code to convert the input files. Will finish this once the economics output is the same.

Also once a model is running with the new code check the warnings to make sure no arrays are filling to the end when they shouldn’t be.

4-Feb-2018

init_scalar - This will now apply scalars to biomass pools as well as vertebrate numbers (but not detritus).