Problems with npzd_Powell

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gabrielanalini
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Location: Universidade Federal Fluminense

Problems with npzd_Powell

#1 Post by gabrielanalini » Mon Jan 04, 2016 6:03 pm

Hi!

I am studying the response of phytoplankton community to eddy activity in Brazilian Southeast coast.

My hydrodinamic model is working fine, the problem happens with the npzd_Powell model. I made tests with both homogeneus initial conditions and idealized npzd fields. There seems to be no response or interaction between the npzd compartments.The vertical structure for physical variables works, but for the biological parameters not.

I made a run using the upwelling testcase with npzd_Powell active and everything seems to be fine, with instant response from the compartments.

Is there something else to set in the CP or .in for the coupling works?

I'm sending the .h and .in images and some plots.

I’d appreciate any help with this.

Thanks in advance!
Attachments
eddy.log
(3.78 MiB) Downloaded 145 times
eddy.in
(117.65 KiB) Downloaded 195 times
eddy.h
(1.88 KiB) Downloaded 175 times
dayno3_001.png
dayno3_001.png (9.43 KiB) Viewed 8576 times
dayno3_003.png
dayno3_003.png (9.43 KiB) Viewed 8576 times
no3_step8.png
no3_step8.png (55.06 KiB) Viewed 8576 times
dayVz_002.png

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kate
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Re: Problems with npzd_Powell

#2 Post by kate » Mon Jan 04, 2016 6:11 pm

First, you should find out why the colorbar for the first two vertical slice plots wants to extend to 1.e37. Are those points in the land mask?

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wilkin
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Re: Problems with npzd_Powell

#3 Post by wilkin » Tue Jan 05, 2016 4:43 am

Your log file shows the following:
Metrics information for Grid 01:
===============================

Minimum X-grid spacing, DXmin = 0.00000000E+00 km
Maximum X-grid spacing, DXmax = 2.97235216E+00 km
Minimum Y-grid spacing, DYmin = 0.00000000E+00 km
Maximum Y-grid spacing, DYmax = 2.97199962E+00 km
Minimum Z-grid spacing, DZmin = 0.00000000E+00 m
Maximum Z-grid spacing, DZmax = 3.91620893E+02 m
That's odd that you have zero as the minimum grid spacings in all dimensions.

Have you applied special/missing values in the land mask points of the grid metrics? I don't think ROMS will like that.
John Wilkin: DMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559 jwilkin@rutgers.edu

gabrielanalini
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Joined: Sat Nov 29, 2014 3:48 pm
Location: Universidade Federal Fluminense

Re: Problems with npzd_Powell

#4 Post by gabrielanalini » Wed Jan 13, 2016 11:23 pm

Thank you very much for the replies Kate and Wilkin.

Kate, there is no land mask on the biological initial fields, I'm working on this.


Wilkin, I don't know why this is happening. I used to run my experiments in another machine, using MPI, and the minimum grid-spacing was fine. Now, im using OpenMP in a new machine, but I know people who use OpenMP as well without problems. This could be a problem?

chaoyu1985
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Location: south china sea institute of oceanography

Re: Problems with npzd_Powell

#5 Post by chaoyu1985 » Tue Sep 26, 2017 7:14 am

gabrielanalini wrote:Thank you very much for the replies Kate and Wilkin.

Kate, there is no land mask on the biological initial fields, I'm working on this.


Wilkin, I don't know why this is happening. I used to run my experiments in another machine, using MPI, and the minimum grid-spacing was fine. Now, im using OpenMP in a new machine, but I know people who use OpenMP as well without problems. This could be a problem?
Hi, i am runing npzd as well. How did u give the boundary condition (i.e.alkalinity,NH4,SDeN). In my study area,NH4 data is absent. I can not find any other reanalysis data from internet. So,I used a constent value for all grids and boundary condition. the model can not run sucessuflly. How did you set the boundary condition in the time series. did they vary with time ? did they match with the changes of the chlorophyll and phytoplankton? thank you so much for your help.

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