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<div class="title">Lake Jersey Nesting Refinement Examples</div>__NOTOC__

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==Description==

The Lake Jersey test case is primarily used to evaluate the nesting algorithms for the Refinement Grids Super-Class. It is activated with C-preprocessing options [[Options#LAKE_JERSEY|LAKE_JERSEY]] and [[Options#NESTING|NESTING]]. The nesting algorithms in ROMS are two-way by default.  The option [[Options#ONE_WAY|ONE_WAY]] can be used for just one-way exchange between donor ('''dg''') and receiver ('''rg''') grids. However, the one-way exchange has no effect whatsoever on the coarser donor grid because there is no feed back of information. Notice that due to its higher spatial and temporal resolutions, the finer grid is better resolving the physical phenomena at smaller scales.

This example is a double refinement application with four grids: coarse ('''a'''), and 3 refinements ('''b''', '''d''', and '''c''').  There are six contact regions ('''cr''') and three nesting layers because three different time-step sizes are required in <span class="forestGreen">roms_lake_jersey_nested_4g_abdc.in</span>:


* Number of nested grids.<div class="box">      [[Variables#Ngrids|Ngrids]] =  4</div>

* Number of grid nesting layers.  This parameter is used to allow refinement and composite grid combinations.<div class="box">  [[Variables#NestLayers|NestLayers]] =  3</div>
	
* Number of grids in each nesting layer, [1:[[Variables#NestLayers|NestLayers]]] values are expected.<div class="box">[[Variables#GridsInLayer|GridsInLayer]] =  1  2  1</div>

* Time-stepping parameters.<div class="box">      [[Variables#ntimes|NTIMES]] == 1920      5760      5760     9600<br />          [[Variables#dt|DT]] == 90.0d0    30.0d0    30.0d0   18.0d0<br />     [[Variables#ndtfast|NDTFAST]] == 30        30        30       30</div>

* Input NetCDF file names, [1:[[Variables#Ngrids|Ngrids]]] values are expected. The order of the grids are extremely important in nesting applications.<div class="box">     [[Variables#GRD|GRDNAME]] == ../Data/lake_jersey_grd_a.nc      \<br />                ../Data/lake_jersey_grd_b.nc      \<br />                ../Data/lake_jersey_grd_d.nc      \<br />                ../Data/lake_jersey_grd_c.nc <br /><br />     [[Variables#INI|ININAME]] == ../Data/lake_jersey_ini_a.nc      \<br />                ../Data/lake_jersey_ini_b.nc      \<br />                ../Data/lake_jersey_ini_d.nc      \<br />                ../Data/lake_jersey_ini_c.nc <br /></div>

* Nesting grids connectivity data: contact points information. This NetCDF file is special and complex. It is currently generated using the script [[contact.m|matlab/grid/contact.m]] from the Matlab repository.<div class="box">     [[Variables#NGCname|NGCNAME]] =  ../Data/lake_jersey_ngc_4g_abdc.nc</div>

* Notice that since the coarse grid ('''a''') is an enclosed basin, all lateral boundary conditions on that grid are set to closed ('''Clo''') while the refined grids ('''b''', '''d''', and '''c'''), which are entirely enclosed by the coarse grid, have nested ('''Nes''') lateral boundary conditions.<div class="box">   [[Variables#LBC|LBC(isFsur)]] ==   Clo     Clo     Clo     Clo \       ! free-surface,  Grid 1<br />                    Nes     Nes     Nes     Nes \       ! free-surface,  Grid 2<br />                    Nes     Nes     Nes     Nes \       ! free-surface,  Grid 3<br />                    Nes     Nes     Nes     Nes         ! free-surface,  Grid 4<br /><br />   [[Variables#LBC|LBC(isUbar)]] ==   Clo     Clo     Clo     Clo \       ! 2D U-momentum, Grid 1<br />                    Nes     Nes     Nes     Nes \       ! 2D U-momentum, Grid 2<br />                    Nes     Nes     Nes     Nes \       ! 2D U-momentum, Grid 3<br />                    Nes     Nes     Nes     Nes         ! 2D U-momentum, Grid 4<br /><br />   [[Variables#LBC|LBC(isVbar)]] ==   Clo     Clo     Clo     Clo \       ! 2D V-momentum, Grid 1<br />                    Nes     Nes     Nes     Nes \       ! 2D V-momentum, Grid 2<br />                    Nes     Nes     Nes     Nes \       ! 2D V-momentum, Grid 3<br />                    Nes     Nes     Nes     Nes         ! 2D V-momentum, Grid 4<br /><br />   [[Variables#LBC|LBC(isUvel)]] ==   Clo     Clo     Clo     Clo \       ! 3D U-momentum, Grid 1<br />                    Nes     Nes     Nes     Nes \       ! 3D U-momentum, Grid 2<br />                    Nes     Nes     Nes     Nes \       ! 3D U-momentum, Grid 3<br />                    Nes     Nes     Nes     Nes         ! 3D U-momentum, Grid 4<br /><br />   [[Variables#LBC|LBC(isVvel)]] ==   Clo     Clo     Clo     Clo \       ! 3D V-momentum, Grid 1<br />                    Nes     Nes     Nes     Nes \       ! 3D V-momentum, Grid 2<br />                    Nes     Nes     Nes     Nes \       ! 3D V-momentum, Grid 3<br />                    Nes     Nes     Nes     Nes         ! 3D V-momentum, Grid 4<br /><br />   [[Variables#LBC|LBC(isMtke)]] ==   Clo     Clo     Clo     Clo \       ! mixing TKE,    Grid 1<br />                    Nes     Nes     Nes     Nes \       ! mixing TKE,    Grid 2<br />                    Nes     Nes     Nes     Nes \       ! mixing TKE,    Grid 3<br />                    Nes     Nes     Nes     Nes         ! mixing TKE,    Grid 4<br /><br />   [[Variables#LBC|LBC(isTvar)]] ==   Clo     Clo     Clo     Clo \       ! temperature,   Grid 1<br />                    Clo     Clo     Clo     Clo \       ! salinity,      Grid 1<br />                    Nes     Nes     Nes     Nes \       ! temperature,   Grid 2<br />                    Nes     Nes     Nes     Nes \       ! salinity,      Grid 2<br />                    Nes     Nes     Nes     Nes \       ! temperature,   Grid 3<br />                    Nes     Nes     Nes     Nes \       ! salinity,      Grid 3<br />                    Nes     Nes     Nes     Nes \       ! temperature,   Grid 4<br />                    Nes     Nes     Nes     Nes         ! salinity,      Grid 4<br /></div> 


The following tables summarize the nested grids information:


<div style="padding-left: 25px">
{| id="grids" border="1" cellspacing="0" cellpadding="5" align="left"
! colspan="6" | Grid Information
|-
!Grid
!ng
!Mesh<br />Size
!Refinement<br />Factor
!&Delta;x<br />&Delta;y
!dt<br />(s)
|-
|align="center" | '''a'''
|align="center" | 1
|align="right"  | 100x80x8
|align="center" | <nowiki>-</nowiki>
|align="right"  | 500.0 m
|align="center" | 90.0
|-
|align="center" | '''b'''
|align="center" | 2
|align="right"  | 66x99x8
|align="center" | 1:3 from '''a'''
|align="center" | 166.6 m
|align="center" | 30.0
|-
|align="center" | '''d'''
|align="center" | 3
|align="right"  | 114x60x8
|align="center" | 1:3 from '''a'''
|align="center" | 166.6 m
|align="center" | 30.0
|-
|align="center" | '''c'''
|align="center" | 4
|align="right"  | 120x130x8
|align="center" | 1:5 from '''a'''
|align="center" | 100.0 m
|align="center" | 18.0
|}

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{| id="contact" border="1" cellspacing="0" cellpadding="5" align="left"
!colspan="3" | Contact Region Information
|-
!cr
!dg
!rg
|-
|align="center" | 1
|align="center" | 1 ('''a''')
|align="center" | 2 ('''b''')
|-
|align="center" | 2
|align="center" | 1 ('''a''')
|align="center" | 3 ('''d''')
|-
|align="center" | 3
|align="center" | 1 ('''a''')
|align="center" | 4 ('''c''')
|-
|align="center" | 4
|align="center" | 2 ('''b''')
|align="center" | 1 ('''a''')
|-
|align="center" | 5
|align="center" | 3 ('''d''')
|align="center" | 1 ('''a''')
|-
|align="center" | 6
|align="center" | 4 ('''c''')
|align="center" | 1 ('''a''')
|}

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The Nested Grids Connectivity (NGC) input NetCDF file is created in Matlab using the following commands:

 <span class="twilightBlue"> >>  Gnames = {'lake_jersey_grd_a.nc', 'lake_jersey_grd_b.nc', 'lake_jersey_grd_d.nc', 'lake_jersey_grd_c.nc'};<br \> >>  Cname  = 'lake_jersey_ngc_4g_abdc.nc';<br \> >>  [S,G] = contact(Gnames, Cname);</span>

This creates several figures with useful information. Users need to download the [[Grid_Processing_Scripts | grid processing scripts]] from ROMS Matlab repository.  This Matlab script is quite complex because the nested connectivity is not trivial and is done outside of ROMS for efficiency. See the following [[Nested_Grids|pages for detailed information and diagrams]].

==Results==

The plots below show the results after 2 days of simulation for one-way and two-way nesting configurations. They are plotted with Matlab using the script plot_nesting.m. The refined solutions ('''b''', '''d''', and '''c''') are overlayed on top of the coarse grid ('''a'''). The color map is rendered using shading flat, meaning there is no interpolation between pixels in the color maps. <span class="orange">Click the figure to see a more detailed image. On the resulting page a link to the full resolution image is provided</span>.

The figures below were created in Matlab using the following commands:

 <span class="twilightBlue"> >>  Gnames = {'lake_jersey_grd_a.nc', 'lake_jersey_grd_b.nc', 'lake_jersey_grd_d.nc', 'lake_jersey_grd_c.nc'};<br \> >>  Anames = {'lake_jersey_avg_a.nc', 'lake_jersey_avg_b.nc', 'lake_jersey_avg_d.nc', 'lake_jersey_avg_c.nc'};<br \> >>  Hnames = {'lake_jersey_his_a.nc', 'lake_jersey_his_b.nc', 'lake_jersey_his_d.nc', 'lake_jersey_his_c.nc'};<br \> >><br \> >>  G = grids_structure (Hnames, Hnames);<br \> >><br \> >>  F = plot_nesting (G, Hnames, 'temp', 97, 8, 1, true);<br \> >>  F = plot_nesting (G, Hnames, 'salt', 97, 8, 1, true);<br \> >>  F = plot_nesting (G, Hnames, 'zeta', 97, 8, 1, true);<br \> >><br \> >>  F = plot_nesting (G, Anames, 'rvorticity_bar', 97, 8, 1, true);<br \></span>

Again, users need to download these scripts from the ROMS Matlab repository.


<gallery widths=500px heights=350px perrow=2 caption="Surface Temperature (Celsius)">
Image:lake_jersey_temp_oneway_4g_abdc.png|<center>One-way</center>
Image:lake_jersey_temp_twoway_4g_abdc.png|<center>Two-way</center>
</gallery>


<gallery widths=500px heights=350px perrow=2 caption="Surface Salinity">
Image:lake_jersey_salt_oneway_4g_abdc.png|<center>One-way</center>
Image:lake_jersey_salt_twoway_4g_abdc.png|<center>Two-way</center>
</gallery>


<gallery widths=500px heights=350px perrow=2 caption="Free-surface (m)">
Image:lake_jersey_zeta_oneway_4g_abdc.png|<center>One-way</center>
Image:lake_jersey_zeta_twoway_4g_abdc.png|<center>Two-way</center>
</gallery>


<gallery widths=500px heights=350px perrow=2 caption="3-minute Averaged Vertically Integrated Relative Vorticity (1/s)">
Image:lake_jersey_rvorticity_bar_oneway_4g_abdc.png|<center>One-way</center>
Image:lake_jersey_rvorticity_bar_twoway_4g_abdc.png|<center>Two-way</center>
</gallery>