Merge pull request #107 from schism-dev/hotfix/param

update param.nml

pyschism/param/param.nml

@@ -158,16 +158,19 @@
 
 !-----------------------------------------------------------------------
 ! 2nd stabilization method via Shapiro filter. This should normally be used 
-! if indvel=0. To transition between eddying/non-eddying regimes, use
+! if indvel=0. ishapiro=0: off; =1: constant filter strength in shapiro0; =-1:
+! variable filter strength specified in shapiro.gr3; =2: variable filter strength specified
+! as a Smagorinsky-like filter, with the coefficient specified in shapiro.gr3.
+! To transition between eddying/non-eddying regimes, use
 ! indvel=0, ihorcon/=0, and ishapiro=-1 (requiring shapiro.gr3) or 2 (Smagorinsky-like filter).
 !-----------------------------------------------------------------------
   ishapiro = 1 !options
   niter_shap = 1 !needed if ishapiro/=0: # of iterations with Shapiro filter
-  !shapiro0: Shapiro filter strength, needed only if ishapiro=1 or 2 
+  !shapiro0: Shapiro filter strength, needed only if ishapiro=1 
   !If ishapiro=1, shapiro0 is the filter strength (max is 0.5).
-  !If ishapiro=2, shapiro0 is the coefficient in tanh(). Experiences so far suggest ~1.e3
-  !If ishapiro=-1, this is not used as the filter strength is read in from shapiro.gr3
-  shapiro0 = 0.5 
+  !If ishapiro=2, the coefficient in tanh() is specified in shapiro.gr3. Experiences so far suggest 100 to 1.e3
+  !If ishapiro=-1, the filter strength is directly read in from shapiro.gr3
+  shapiro0 = 0.5 !needed only if ishapiro=1
 
 !-----------------------------------------------------------------------
 ! Implicitness factor (0.5<thetai<=1).
@@ -284,20 +287,26 @@
 
 ! meth_sink: options to treat sinks @ dry elem: no speacial treatment if meth_sink=0;
 ! zero out sink if the elem is dry if meth_sink=1
+! If USE_NWM_BMI is on with if_source/=0, some parts of the reading and some b.c. will be bypassed (but the inputs
+! will still be needed).
 !-----------------------------------------------------------------------
   if_source = 0
 !  nramp_ss = 1 !needed if if_source=1; ramp-up flag for source/sinks
   dramp_ss = 2 !needed if if_source/=0; ramp-up period in days for source/sinks (no ramp-up if <=0)
   meth_sink = 1 !options to treat sinks @ dry elem
 
+!----------------------------------------------------------------------
 ! Specify vertical level to inject source concentration for each tracer _module_.
 ! Code will extrapolate below bottom/above surface unless level 0 is specified. In
 ! the latter case, the incoming tracer mass will be distributed across all vertical layers - 
 ! this approach works best in shallow waters. 
+! NOTE: AGE module has its own way of injecting age tracers, so make sure the age concentrations
+!  are all -9999. in msource.th so as to not interfere!
+!----------------------------------------------------------------------
   lev_tr_source(1) = -9 !T
   lev_tr_source(2) = -9 !S
   lev_tr_source(3) = -9 !GEN
-  lev_tr_source(4) = -9 !AGE
+  lev_tr_source(4) = -9 !AGE: set -9999. in msource's AGE section
   lev_tr_source(5) = -9 !SED3D
   lev_tr_source(6) = -9 !EcoSim
   lev_tr_source(7) = -9 !ICM
@@ -307,6 +316,11 @@
   lev_tr_source(11) = -9 !FABM
   lev_tr_source(12) = -9 !DVD
 
+!----------------------------------------------------------------------
+! Specify level #'s if age module is invoked (USE_AGE), for 1st half of tracers only
+!----------------------------------------------------------------------
+  level_age = 9, -999 !default: -999 (all levels)
+
 !-----------------------------------------------------------------------
 ! Horizontal diffusivity option. if ihdif=1, horizontal diffusivity is given in hdif.gr3
 !-----------------------------------------------------------------------
@@ -339,7 +353,9 @@
   coricoef = 0 !if ncor=0
 
 !-----------------------------------------------------------------------
-! Elevation initial condition flag for cold start only. If ic_elev=1, elev.ic (in *.gr3 format) is needed
+! Elevation initial condition flag for cold start only. For hotstart, set this to 0
+! (and elev will be read in from hotstart.nc).
+! If ic_elev=1, elev.ic (in *.gr3 format) is needed
 ! to specify the initial elevations; otherwise elevation is initialized to 0 everywhere 
 !-----------------------------------------------------------------------
   ic_elev = 0
@@ -511,18 +527,18 @@
   small_elad = 1.e-4  !small (inactive at the moment)
 
 !-----------------------------------------------------------------------
-! Atmos. option. nws=3 is reserved for coupling with atmospheric model.
+! Atmos. option. Use nws=2 and USE_ATMOS for coupling with atmospheric model.
 ! If nws=0, no atmos. forcing is applied. If nws=1, atmos.
 ! variables are read in from wind.th. If nws=2, atmos. variables are
 ! read in from sflux_ files.
 ! If nws=4, ascii format is used for wind and atmos. pressure at each node (see source code).
 ! If nws=-1 (requires USE_PAHM), use Holland parametric wind model (barotropic only with wind and atmos. pressure).
 !  In this case, the Holland model is called every step so wtiminc is not used. An extra 
-!  input is needed: hurricane-track.dat
+!  input file is needed: hurricane-track.dat, in addition to a few parameters below.
 !
 ! Stress calculation:
 ! If nws=2, ihconsv=1 and iwind_form=0, the stress is calculated from heat exchange
-! routine; 
+! routine; in this case USE_ATMOS cannot be on.
 ! Otherwise if iwind_form=-1, the stress is calculated from Pond & Pichard formulation;
 ! if iwind_form=1, Hwang (2018) formulation (Cd tapers off at high wind).
 ! If WWM is enabled and icou_elfe_wwm>0 and iwind_form=-2 or -3, stress is overwritten by WWM:
@@ -536,6 +552,8 @@
   drampwind = 1. !ramp-up period in days for wind (no ramp-up if <=0)
   iwindoff = 0 !needed only if nws/=0; '1': needs windfactor.gr3
   iwind_form = 1 !needed if nws/=0
+  model_type_pahm=10 !only used if nws=-1: hurricane model type (1: Holland; 10: GAHM)
+
   !If IMPOSE_NET_FLUX is on and nws=2, read in net _surface_ heat flux as var 'dlwrf' 
   !(Downward Long Wave) in sflux_rad (solar radiation is still used separately),
   !and if PREC_EVAP is on, also read in net P-E as 'prate' (Surface Precipitation Rate) in sflux_prc.
@@ -642,13 +660,13 @@
   iharind = 0
 
 !-----------------------------------------------------------------------
-! Conservation check option. If iflux=1, some fluxes are computed
-! in regions specified in fluxflag.prop (regional number from -1 to an arbitrary integer).
-! in output flux.out, positive means flux from region n to region n-1 (n>=1)
-! output file flux.dat need to be saved before continuing hotstart
+! Conservation check option. If iflux/=0, some fluxes are computed
+! in regions specified in fluxflag.prop (regional number from -1 to an arbitrary integer)
+! in output flux.out, positive means flux from region n to region n-1 (n>=1).
+! Output file flux.out will be appended on ihot=2.
+! iflux=1: basic output; =2: more elaborate outputs
 !-----------------------------------------------------------------------
   iflux = 0
-  iflux_out_format = 0 !0: basic flux output; 1: more detailed outputs
 
 !-----------------------------------------------------------------------
 ! Test flags for debugging. These flags should be turned off normally.
@@ -701,11 +719,6 @@
   nstep_ice = 1 !call ice module every nstep_ice steps of SCHISM
 
 
-!----------------------------------------------------------------------
-! Specify level #'s if age module is invoked (USE_AGE), for 1st half of tracers only
-!----------------------------------------------------------------------
-  level_age = 9, -999 !default: -999 (all levels)
-
 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 ! Physical constants
 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -780,7 +793,7 @@
 !-----------------------------------------------------------------------
 ! Option for hotstart outputs
 !-----------------------------------------------------------------------
-  nhot = 0 !1: output *_hotstart every 'hotout_write' steps
+  nhot = 0 !1: output *_hotstart every 'nhot_write' steps
   nhot_write = 8640 !must be a multiple of ihfskip if nhot=1
 
 !-----------------------------------------------------------------------
@@ -1074,7 +1087,7 @@
 !-----------------------------------------------------------------------
 ! Ice module outputs (if USE_ICE is on)
 !-----------------------------------------------------------------------
-!  iof_ice(1)= 0 !strain rate @ elem [1/sec] {iceStrainRate}  2D
+!  iof_ice(1)= 0 !divergence @ elem ('Delta') [1/sec] {iceStrainRate}  2D
 !  iof_ice(2)= 0 !ice advective velcoity vector [m/s] {iceVelocityX,Y}  2D vector
 !  iof_ice(3)= 0 !net heat flux to ocean (>0 warm up SST) [W/m/m] {iceNetHeatFlux}  2D
 !  iof_ice(4)= 0 !net fresh water flux to ocean (>0 freshens up SSS) [kg/s/m/m] {iceFreshwaterFlux}  2D