Restart with biology

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Restart with biology

#1 Post by Virivarola » Mon Oct 28, 2013 6:36 pm


I have a problem with using RESTART, I am running a 2D case with Fennel´s bio-model.
I used NRREC=-1 and DSTART=730 (days) (the last time of my restart file.)
The model physics seems to continue the previous solution, but the biological component does not. Actually all biological variables are set to (and remain) zero.
I tried to figure out what´s going on but I can´t see it - I am pretty new here..

Could you help me with this?

Thanks in advance,

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Re: Restart with biology

#2 Post by kate » Mon Oct 28, 2013 7:17 pm

I'm surprised you got as far as you did trying to run an ecosystem model in a 2-D simulation. There are many places in the code - including get_state.F - where all tracers are contained within #ifdef SOLVE3D.


Re: Restart with biology

#3 Post by Virivarola » Mon Oct 28, 2013 7:42 pm

Hi Kate,

Thank you for replying.
It is a quasi-2D configuration, I am using NS-periodic bd conditions.
I have also included #ifdef SOLVE3D in my include file. First, I started
analizing the BIO_TOY case and I thought a 2D configuration could work in a rather similar way..
But if there is something I'm missing and you could orientate me a bit, I´d really appreciate it.


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Re: Restart with biology

#4 Post by LauraB » Tue Oct 29, 2013 12:56 pm

Hi Virginia,

As far as I understand it, you don't need to change DSTART when you re-start a run, just NRREC. Hope that helps!


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Re: Restart with biology

#5 Post by wilkin » Tue Oct 29, 2013 2:05 pm

Don't change DSTART when you continue a simulation. That will alter the filename numbering and potentially overwrite your previous results.

The thing to check is what standard output (a.k.a. the logfile) reports regarding the initial conditions being read on the restart. You should see a line reporting:

Code: Select all

NLM: GET_STATE - Read state initial conditions,             t = .....
                  (Grid 01, File: the file, Rec=0001, Index=1)
               - free-surface
                   (Min = -8.21818829E-01 Max =  1.96565187E+00)
                - vertically integrated u-momentum component
                   (Min = -1.39076531E+00 Max =  1.41531563E+00)
followed by the list of all variables read.

If ROMS is reading the physics but not reading the bio variables then the information in the logfile might point toward the problem.
John Wilkin: DMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559


Re: Restart with biology

#6 Post by Virivarola » Tue Oct 29, 2013 9:05 pm

Thank you all for your help.

Indeed, the log file shows that the biological variables are not being read.
As Kate suggested I should ask that in get_state.F I guess, I´ll try to make it work!

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