Physics Input File
Useful hints:
Scale point source data as its read in by a constant rate.
Turning off the transport model.
Be warned if you turn off the transport model (advect_diffusion = 0) for some reason (debugging) this will stop the t.hd timestep from incrementing. This timestep is the hydro model timstep - this is also used to read in data from the point source input files. So if you turn off the transport model the values read in from teh point source files will always be the value corresponding to the first hydro timestep (the first time value in the first hydro forcing file).
This is a sample physics parameter file with additional comments.
#############################################
# Physics parameters
vdiffwt_wc 1.0 # Fully implicit vertical mixing
vdiffwt_sed 1.0 # Fully implicit vertical mixing
# Tolerance for water column dz values
# The model only allows this much fractional
# change before dz is reset to nominal value
wc_dz_tol 0.20
# Allow 20% change
# PILOT MODEL - constant water column mixing cfft
wc_kz 0.0128
#############################################
# Sediment related parameters
# Maximum and minimum allowed sediment layer thickness
maxseddz 0.5
minseddz 0.1
# Functional form for bioirrigarion and bioturbation activity
# as a function of depth. Currently can be one of:
# constant
# linear
# parabolic
# gaussian
# Only the first letter of this parameter is significant
biosedprofile gaussian
## Functional form for oxygen profile
# as a function of depth. Currently can be one of:
# constant
# linear
# parabolic
# gaussian
# Only the first letter of this parameter is significant
biooxprofile linear
# Diffusion coefficient for bio-irrigation of sediments.
# This value is scaled by the amount of biological
# activity present, and also decreases with depth
# in the sediment according to some
# fixed profile. The value here is the value which
# would apply at zero depth in the sediment.
# Units are m2 s-1 per animal per m2.
# bi_dissol_kz 0.0000001
bi_dissol_kz 0.0000001
# Exchange rate for bio-irrigation of sediments.
# This value is scaled by the amount of biological
# activity present, and also decreases with depth
# in the sediment according to some
# fixed profile. The value here is the value which
# would apply at zero depth in the sediment.
# Units are m s-1 per animal per m2 (in long-winded
# terms this is volume per square metre per second
# per animal per square metre).
# bi_exchange 0.000001
bi_exchange 0.000001
# Injection rate for bio-irrigation of sediments.
# This value is scaled by the amount of biological
# activity present, and also decreases with depth
# in the sediment according to some
# fixed profile. The value here is the value which
# would apply at zero depth in the sediment.
# Units are m s-1 per animal per m2. (in long-winded
# terms this is volume per square metre per second
# per animal per square metre).
bi_injection 1e-8
# Diffusion coefficient for bio-turbation of sediments.
# This value is scaled by the amount of biological
# activity present, and also decreases with depth
# in the sediment according to some
# fixed profile. The value here is the value which
# would apply at zero depth in the sediment.
# Units are m2 s-1 per animal per m2.
bt_partic_kz 0.00000001
# Exchange rate for bio-turbation of sediments.
# This value is scaled by the amount of biological
# activity present, and also decreases with depth
# in the sediment according to some
# fixed profile. The value here is the value which
# would apply at zero depth in the sediment.
# Units are m s-1 per animal per m2 (in long-winded
# terms this is volume per square metre per second
# per animal per square metre).
# bt_exchange 0.000001
bt_exchange 1e-8
# Expulsion rate for bio-irrigation of sediments.
# This value is scaled by the amount of biological
# activity present, and also decreases with depth
# in the sediment according to some
# fixed profile. The value here is the value which
# would apply at zero depth in the sediment.
# Units are m s-1 per animal per m2 (in long-winded
# terms this is volume per square metre per second
# per animal per square metre).
# bt_expulsion 0.000001
bt_expulsion 1e-8
# Limit to errosion rate for a 1 cm sediment model
max_erosion 0.005
#################################################################################
# General physical configuration parameters
#
# Switch indicating whether minimum water column depth constrained to 1m
constrain_wc 0
# Base line temperature for the q10 and seasonal temperature calculations
baseline_temp 21.0
temp_ampltiude 5.5
# Injection rate for vertical upwelling of water column tracers
# This value is scaled by the a box specific upwelling scalar.
mix_injection 1e-3
# Scaling coefficient to capture increased mixing rate in winter
mix_season_kz 10.0
# Deep ocean mixing on or not. Yes = 1 No = 0.
mix_deep 0
Deep ocean mixing for oxygen on or not. Yes = 1 No = 0.
mix_deep_O2 1
Depth for marking deep ocean (boxes deeper than this will get deep ocean mixing)
mix_deep_depth -1200
# Switch to indicate whether or not the injection of materials from
# point sources is used. Yes = 1, No =0.
injection 1
# Switch to indicate whether or not the injection of materials from
# the atmosphere is used. Yes = 1, No =0.
atmospherics 0
# Switch to indicate whether or not the settling model
# added to the transport model is used. Yes = 1, No =0.
settling 0
# Switch to indicate whether or not the bioirrigation model
# added to the transport model is used. Yes = 1, No =0.
bioirrigation 1
# Switch to indicate whether or not the bioturbation model
# added to the transport model is used. Yes = 1, No =0.
bioturbation 1
# Switch to indicate whether or not the vertical diffusion model
# added to the transport model is used. Yes = 1, No =0.
vert_diffusion 0
# Switch to indicate whether or not the horizontal diffusion model
# added to the transport model is used. Yes = 1, No =0.
horiz_diffusion 0
# Switch to indicate whether or not the forced vertical mixing model
# added to the transport model is used. Yes = 1, No =0.
vert_mix 0
# Switch to indicate whether or not the basic advect_diffusion
# (transport) model is used. Yes = 1, No =0.
# Be warned - if this is turned off the hydro timestep will not increment. This means
# the data read in from the point sources files will always be the value in the first hydro timestep.
advect_diffusion 0
# Switch to indicate whether or not the resuspension model
# is used. Yes = 1, No =0.
resuspension 0
# Switch to indicate whether or not the decay model
# is used in the water column. Yes = 1, No =0.
decay_wc 0
# Switch to indicate whether or not the decay model
# is used in the sediment. Yes = 1, No = 0.
decay_sed 1
# Scalar for sediment decay (proxy for additional losses due to burial)
decay_sed_scale 1.0
# Switch to indicate whether or not to scale exchanges. No =0, Yes = 1, Area_corrected = 2.
scale_transport 0
# Coefficient used in constant scaling of exchanges
# (the exchanges are multiplied by this value before they are used)
prcnt_exchange 1.0
# Coefficient used in area corrected scaling of exchanges
# (the area corrected exchanges are multiplied by
# this value before they are used)
ka_exchange 1000
# Switch to indicate whether or not to have cascading flows (exchanges). No =0, Yes = 1
cascade_flows 0
# Switch indicating type of each box (enter 0 for internal boxes and then
# for boundary boxes 0=standard, 1=absorptive, 2=reflective, 3=assymetrical scaling)
edge_type 47
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 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#############################################
# Quarterly vectors of seasonal eddy strength
# (model linearly interpolates between these to get eddy strength on any one day, which
# can be used to condition primary production)
eddy_S1 47
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
eddy_S2 47
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
eddy_S3 47
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
eddy_S4 47
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
# Eddy scaling of vertical mixing
eddy_vertmix 0
# Coefficient used in scaling of vertical exchanges by eddies
eddy_mixscale 10.0
#############################################
## Point source nutrient input related parameters
# Set up for the Clarence so that inputs from the Clarence Coastal catchment are distributed over 7 boxes
# Switch to indicate whether or not gradual nutrient change
# is allowed in the model
nutrientchange 1
# Flag to indicate whether the point source can be scaled
# There must be as many entries here as for npointss in the forcing parameter file
psschange 38
0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
# Switch to indicate whether or not nutrient change
# is constant once increased/decreased or if falls back to original
# i.e. pulsed or not
pulsechange 0
Multiplier which represents degree of total change of the
# nutrients (i.e. 3 => final amt = 3xinitial; 0.3 => final=initial/3)
# There must be a value per point source - so an array of npointss (npointss is defined in your forcing prm #file)
pss_mult 38
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 0 0 0 0.1 0
Period of time over which change in nutrients occurs - must be an array of npointss values.
pss_period 38
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Start day of nutrient increase - must be an array of npointss values.
pss_start 38
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 0 0 0 0 0
Switch to indicate whether or not a second gradual nutrient change
# is allowed in the model
# Note if this is 0 then the following values are not read in - they will just be set to 0 and never used.
nutrientchange2 0
Multiplier which represents size of nutrient levels after second change
# So if to end at 0.5x standard input file levels then this
# value would be 0.5 etc.
# There must be a value per point source - so an array of npointss (npointss is defined in your forcing prm #file)
pss_mult2 38
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 0 0 0 0 0
Period of time over which second change in nutrients occurs
# here = 1 year of model run. This value must be at least 1. - - must be an array of npointss values.
pss_period2 38
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Start day of second change in nutrients - - must be an array of npointss values.
pss_start2 38
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 0 0 0 0 0