[MITgcm-support] What is the use of "gendata.m" in "verification/tutorial_barotropic_gyre"?

Mon Nov 25 08:22:24 EST 2013

The dimensions are i,j,k (for “x”, “y”, “z”) and “time” (the forth dimension), or in diagnostics you might have more than 1 variable, so then, the last dimension (in matlab) is the variable index (see your data.diagnostics for what you saved)

gendata.m is just an example of how you can create initial and boundary conditions. If you want to simulate something the the sourth china sea, you’ll have to generate bathymetry, initial and boundary conditions yourself. How you do that is completely up to you; you can use matlab or anything else.
The MITgcm requires ieee big endian unblocked files as input (an the gendata.m’s show you how to genererate them with matlab), that’s what you have to make sure to do when you generate your fields.

Martin

On Nov 25, 2013, at 1:26 PM, Moon <lzl124631x at 163.com> wrote:

> Hi Martin,
> 
> Many thanks for your patience! As a neophyte of MITgcm, I still have batches of questions (TnT). Hope you will not get bored.
> 
> Actually I have derived an N-soliton solution which can describe internal solitary wave (ISW) and I'm willing to use MITgcm to conduct some simulations on it. But....here come the questions:
> 
> 1) Is it possible to integrate my solution into MITgcm? What should I do?
> 
> 2) I've learned that all the packages used in a specific experiment are wrote in packages.conf. Do you know the minimum set of packages we need while investigating ISW?
> 
> 3) Have you ever modified the 'gendata.m' to get a different result? I now know it's for generating the topography (bathymetry) and/or some other input data of, for example, heat flux and wind stress. What if I want to modify the bathymetry? What if I just want to focus on the South China Sea?
> 
> 4) I've wrote some scripts to automatically visualize the data/meta files in matlab. But I'm confused about the meaning of their dimensions. To my knowledge, their dimensions range from 1 to 4. I use plot for 1D data, imagesc/contourf for 2D data. Temporarily, I decompose 3D data (e.g. T: 90x40x15) into multiple 2D data (e.g. T1~T15: 90x40). I still don't know how to visualize 4D data (e.g. in global_ocean.90x40x15, prefixes gynDiag 90x40x15x6 and oceDiag 90x40x15x6). What are the meaning of its four dimensions?
> 
> Attachments are examples of my output files.
> Thanks in advance! Any help will be appreciated!
> Cordially,
> Moon
> 
> 
> 
> At 2013-11-25 18:59:02,"Martin Losch" <Martin.Losch at awi.de> wrote:
> >Hi Moon,
> >
> >XC, YC are the coordinates of you grid centers/divergence/pressure/skalar points (usually in longitude/latitude, but for cartesian grids in meters relative to some origin), DXC, DYC are the distances between these grid points in meters. The XG,YG are the coordinates of the corner/vorticity points, DXG, DYG the corresponding distances (grid spacing!).
> >RC, RF are the depths of the cell centers (C) and cell faces (F), DRC, DRF are the distances between those (in meters or pressure coordinates).
> >Please, have a look at the head of model/inc/GRID.h which summarizes these grid variables nicely, I believe. That’s also where they are defined.
> >
> >The “PH” variables are the pressure potential anomalies (im m^2/s^2) and these have just been discussed a few days ago. People don’t look at them too often.
> >“ref” in a name stands for “reference”.
> >
> >For tailored output I recommend using the diagnostics package!
> >
> >Martin
> >
> >On Nov 25, 2013, at 9:23 AM, Moon <lzl124631x at 163.com> wrote:
> >
> >> Hi, Jean
> >> Thanks a lot! Embarrassed for missing those words in the user manual. However, after searching through the user manual, I still cannot find the meaning of some prefixes of data/meta files. Below is my summary, with purple denoting those I've found definition, blue denoting those I have not and some other I'm not sure. Can you give me some hints?
> >> Yours Sincerely,
> >> Moon
> >> 
> >> Depth     Bathymetry
> >> DRC     Section 2.11.5
> >> DRF     Section 2.11.5
> >> DXC     Section 2.11.4
> >> DXG     Section 2.11.4
> >> DYC     Section 2.11.4
> >> DYG     Section 2.11.4
> >> Eta     ocean: surface elevation (m), atmosphere: surface pressure anomaly (Pa).
> >> hFacC     Section 2.11.6
> >> hFacS     Section 2.11.6
> >> hFacW     Section 2.11.6
> >> PH
> >> PHL
> >> PHrefC
> >> PHrefF
> >> RAC     Section 2.11.4
> >> RAS     Section 2.11.4
> >> RAW     Section 2.11.4
> >> RAZ     Section 2.11.4
> >> RC     Maybe related to coordinate, but is it saved in DRC?
> >> RF     Maybe related to coordinate, but is it saved in DRF?
> >> RhoRef
> >> S     ocean: salinity (psu), atmosphere: water vapor (g/kg).
> >> T     potential temperature (ocean: C, atmosphere: K).
> >> U     zonal component of velocity field (m/s and positive eastward).
> >> V     meridional component of velocity field (m/s and positive northward).
> >> W     vertical component of velocity field (ocean: m/s and positive upward, atmosphere: Pa/s and positive towards increasing pressure i.e. downward).
> >> XC     Maybe related to coordinate, but is it saved in DXC?
> >> XG     Maybe related to coordinate, but is it saved in DXG?
> >> YC     Maybe related to coordinate, but is it saved in DYC?
> >> YG     Maybe related to coordinate, but is it saved in DXG?
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> At 2013-11-25 00:01:25,"Jean-Michel Campin" <jmc at ocean.mit.edu
> >> > wrote:
> >> >Hi,
> >> >Please take a look at the manual, section 3.9.3.4 and 3.9.3.5
> >> >Jean-Michel
> >> >
> >> >On Fri, Nov 22, 2013 at 11:37:56AM +0800, Moon wrote:
> >> >> What is the use of "gendata.m" in "verification/tutorial_barotropic_gyre"?
> >> >
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