-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathRun_settings.prm
104 lines (87 loc) · 6.84 KB
/
Run_settings.prm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
# Run parameters
verbose 0 # Detailed logged output
flag_sanity_check 1 # Whether the code making sure that overlapping of recruits can't add inappropriately is enabled
flagecon_on 0 # Flag showing whether want economics loaded and submodel run (1) or not (0)
flag_fisheries_on 1 # Flag showing whether want fisheries loaded and submodel run (1) or not (0)
flag_skip_biol 0 # Flag showing whether want biological model run (1) or not (0 - only used when debugging fisheries)
flag_skip_phys 0 # Flag showing whether want biological model run (0) or not (1 - only used when debugging fisheries)
flagpassivetracer 0 # Flag indicating whether passive tracers of advection need to be active in the model
external_populations 0 # FLag indicating whether you want a full population model run for when groups are outside the model domain - 0 = no, 1 = yes
flag_multiyr_migs 0 # Flag indicating whether multi-year (> 1 yr long) migrations need to be included
flag_migration_on 1 # Flag indicating whether any migrations active
debug_it 0
checkbox 0 # Give detailed logged output for this box
checkstart 366666660 day # Start detailed logged output after this date
checkstop 366666660 day # Stop detailed logged output after this date
fishtest 0 # Count up total population for each vertebrate after each main subroutine: 0=no, 1=yes
flaggape 0 # Periodically list prey vs gape statistics (tuning diagnostic)
flagchecksize 1 # Periodically list relative size (tuning diagnostic)
flagagecheck 0 # Periodically list age structure per cohort (tuning diagnostic)
flagdietcheck 0 # Periodically list realised diet matchups (tuning diagnostic)
checkNH 0 # Give detailed logged output for NH in checkbox
checkDL 0 # Give detailed logged output for DL in checkbox
checkDR 0 # Give detailed logged output for DR in checkbox
checkbiom 0 # Give detailed logged output for biomasses in checkbox
which_fleet 35 # ID number of fleet to track (if don't want to track anything set to 33), find number in fisheries input file.
which_check 100 # ID number of group to track (if don't want to track anything set to 80), find number from functional group input file.
habitat_check 0
move_check 67 # ID number of group where tracking movements
fishmove 1 # Set to 0 to turn vertebrate movement off for debugging purposes
debug 0 # 0=debuging off, 1=debug fishing, 2=debug discards, 3=debug histfishing,
# 4=debug assessments, 5=debug mpas, 6=debug effort, 7=debug econ, 8=debug aging,
# 9=debug_spawning, 10=debug migration, 11=debug movement, 12=debug stocks,
# 13=debug biomass calcs, 14=debug feeding, 15=debug everything
title SE Tasmania model with constant forced fishing and base level fishing pressure on FMM increased 2000 fold
dt 12 hour # 12 hour time step
tstop 20 day # Stop time after the given period 15000 5000
toutstart 0 day # Output start time
toutinc 1 day # Write output with this periodicity
toutfinc 1 day # Write fisheries output with this periodicity
tburnday 0 day
check_dups 0 # 1 to check for duplicates in your prm files. Turning this on will make file read in very very slow. Only turn on every once in a while and turn off once the duplicates have been removed.
tsumout 1 day # Write stock state summary with this periodicity
flagannual_Mest 0 # Whether to write out estimates of mortality per predator annually (1) or not (0)
fishout 1 # Switch to turn fisheries output on = 1, off = 0
flagreusefile 2 # Switch to show want to append output file no = 0, yes = 1, replace = 2
flag_age_output 1
# Parameters defining the numbers of certain types of groups (needed to parameter arrays in the
# initialisation section of the model, best left untouched for now)
K_num_tot_sp 62 # total number of biological groups in the model - must match the number of groups defined in your functional group definition file.
K_num_stocks_per_sp 4 # maximum number of stocks per group in the model
K_num_bed_types 3 # maximum number of seabed types (currently only reef, soft and flat) 3
K_num_cover_types 10 # maximum number of habitat types. Should be equal to K_num_bed_types + number of cover groups in your function def input file + 1( canyons ).
K_num_detritus 3 # Total number of detritus groups in the model (labile and refractory and carrion)
# Parameters defining the numbers of certain types of fisheries
# (needed to parameter arrays in the initialisation section of the model,
# best left untouched for now)
K_num_fisheries 33 # Maximum number of fisheries - must match the number of fisheries defined in your fisheries definition input file.
K_num_ports 17 # Maxiumum number of ports in the model area
K_max_num_zoning 1 # Maximum number of spatial zonings used in the model
K_num_reg 2 # Maximum number of management zonings used in the model
K_num_markets 2 # Maxiumum number of markets in the model area
K_num_catchqueue 7 # Length (in days) of list of catches used in running average to give recent CPUE for effort model 8
# Location parameters
flaghemisphere 0 # Flag for hemisphere model is in (0 = southern; 1 = northern)
flagIsEstuary 0 # Flag to indicate if the model is estuary. If true a sediment tracer is required in the initial conditions input file.
flagIsPolar 0 # Flag indicating polar - so there will be 24 hrs of daylight/night seasonally
# Parameters for rescalingin inital vertebrate densities - only for use in emergencies,
# should really update the cdf file instead
flagscaleinit 1 # Flag to indicate whether scaling initial vertebrate densities (1=yes, 0=no)
# Multiplicative scalr for vertebrate initial densities (as read-in from cdf file) Only values for vertebrates used. Order matches functional group definition file.
init_scalar 62
1 1 1 1 1 1 1 1 2 1 1 1 0.1 1 0.5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 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
trackAtomicRatio 0
track_rugosity_arag 0 # flag indicating that rugosity and aragonite saturation to be tracked - needed for coral
track_pH 0 1 # Flag indicating that want to track pH
mirror_invalid 0
track_contaminants 0
flag_pollutant_impacts 0
# See the manual for more info
flag_replicated_old 1
external_box 0
flagAllowLand 0
flag_old_embryo_init 1 #This flag is to allow legacy models to have the same starting conditions under the new code as they did in older version
flag_replicate_old_calendar 1 #This flag specifically allows for legacy models and the influence of environment on the distribution of recruits to be replicated in the newer code
flag_use_deltaH 0
store_aggregate_yoy 0
store_mig_array 0