Changeset 14644 for NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex
- Timestamp:
- 2021-03-26T15:33:49+01:00 (3 years ago)
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- NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final
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NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex
r14200 r14644 6 6 \label{apdx:DOMCFG} 7 7 8 % {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains } \\9 10 \thispagestyle{plain}11 12 8 \chaptertoc 13 9 … … 16 12 {\footnotesize 17 13 \begin{tabularx}{\textwidth}{l||X|X} 18 Release & Author(s) & Modifications\\19 \hline 20 {\em 4.0} & {\em ...} & {\em ...} \\21 {\em 3.6} & {\em ...} & {\em ...} \\22 {\em 3.4} & {\em ...} & {\em ...} \\23 {\em <=3.4} & {\em ...} & {\em ...}14 Release & Author(s) & Modifications \\ 15 \hline 16 {\em next} & {\em Pierre Mathiot} & {\em Add ice shelf and closed sea option description } \\ 17 {\em 4.0} & {\em Andrew Coward} & {\em Creation from materials removed from \autoref{chap:DOM} 18 that are still relevant to the DOMAINcfg tool 19 when setting up new domains } 24 20 \end{tabularx} 25 21 } … … 46 42 47 43 \begin{listing} 48 % \nlst{namdom_domcfg}49 44 \begin{forlines} 50 45 !----------------------------------------------------------------------- … … 91 86 \item [{\np{jphgr_mesh}{jphgr\_mesh}=0}] The most general curvilinear orthogonal grids. 92 87 The coordinates and their first derivatives with respect to $i$ and $j$ are provided 93 in a input file (\ ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module.88 in a input file (\textit{coordinates.nc}), read in \rou{hgr\_read} subroutine of the domhgr module. 94 89 This is now the only option available within \NEMO\ itself from v4.0 onwards. 95 90 \item [{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below). … … 156 151 The reference coordinate transformation $z_0(k)$ defines the arrays $gdept_0$ and 157 152 $gdepw_0$ for $t$- and $w$-points, respectively. See \autoref{sec:DOMCFG_sco} for the 158 S-coordinate options. As indicated on \autoref{fig:DOM_index_vert} \ jp{jpk} is the number of159 $w$-levels. $gdepw_0(1)$ is the ocean surface. There are at most \ jp{jpk}-1 $t$-points153 S-coordinate options. As indicated on \autoref{fig:DOM_index_vert} \texttt{jpk} is the number of 154 $w$-levels. $gdepw_0(1)$ is the ocean surface. There are at most \texttt{jpk}-1 $t$-points 160 155 inside the ocean, the additional $t$-point at $jk = jpk$ is below the sea floor and is not 161 156 used. The vertical location of $w$- and $t$-levels is defined from the analytic … … 167 162 168 163 It is possible to define a simple regular vertical grid by giving zero stretching 169 (\np[=0]{ppacr}{ppacr}). In that case, the parameters \ jp{jpk} (number of $w$-levels)164 (\np[=0]{ppacr}{ppacr}). In that case, the parameters \texttt{jpk} (number of $w$-levels) 170 165 and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. 171 166 … … 179 174 \end{gather} 180 175 181 where $k = 1$ to \ jp{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels. Such an176 where $k = 1$ to \texttt{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels. Such an 182 177 expression allows us to define a nearly uniform vertical location of levels at the ocean 183 178 top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). … … 227 222 \end{equation} 228 223 229 With the choice of the stretching $h_{cr} = 3$ and the number of levels \ jp{jpk}~$= 31$,224 With the choice of the stretching $h_{cr} = 3$ and the number of levels \texttt{jpk}~$= 31$, 230 225 the four coefficients $h_{sur}$, $h_0$, $h_1$, and $h_{th}$ in 231 226 \autoref{eq:DOMCFG_zgr_ana_2} have been determined such that \autoref{eq:DOMCFG_zgr_coef} … … 245 240 Values from $3$ to $10$ are usual. 246 241 \item \np{ppkth}{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 247 (nondimensional, usually of order 1/2 or 2/3 of \ jp{jpk})242 (nondimensional, usually of order 1/2 or 2/3 of \texttt{jpk}) 248 243 \item \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters). 249 244 \item \np{pphmax}{pphmax}: total depth of the ocean (meters). … … 251 246 252 247 As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are: 253 \ jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$,248 \texttt{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 254 249 \np{pphmax}{pphmax}~$= 5750~m$. 255 250 … … 346 341 This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 347 342 \item [{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed). 348 The \ ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at343 The \textit{bathy\_meter.nc} file (Netcdf format) provides the ocean depth (positive, in meters) at 349 344 each grid point of the model grid. 350 345 The bathymetry is usually built by interpolating a standard bathymetry product (\eg\ ETOPO2) onto … … 352 347 Defining the bathymetry also defines the coastline: where the bathymetry is zero, 353 348 no wet levels are defined (all levels are masked). 354 355 The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at356 each grid point of the model grid.357 This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}.358 Defining the ice shelf draft will also define the ice shelf edge and the grounding line position.359 349 \end{description} 360 350 … … 396 386 bathymetry varies by less than one level thickness from one grid point to the next). The 397 387 reference layer thicknesses $e_{3t}^0$ have been defined in the absence of bathymetry. 398 With partial steps, layers from 1 to \ jp{jpk}-2can have a thickness smaller than388 With partial steps, layers from 1 to \texttt{jpk-2} can have a thickness smaller than 399 389 $e_{3t}(jk)$. 400 390 401 The model deepest layer (\ jp{jpk}-1) is allowed to have either a smaller or larger391 The model deepest layer (\texttt{jpk-1}) is allowed to have either a smaller or larger 402 392 thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 403 393 … … 418 408 419 409 \begin{listing} 420 % \nlst{namzgr_sco_domcfg}421 410 \caption{\forcode{&namzgr_sco_domcfg}} 422 411 \label{lst:namzgr_sco_domcfg} … … 592 581 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 593 582 583 \section{Ice shelf cavity definition} 584 \label{subsec:zgrisf} 585 586 If the under ice shelf seas are opened (\np{ln_isfcav}{ln\_isfcav}), the depth of the ice shelf/ocean interface has to be include in 587 the \textit{isfdraft\_meter} file (Netcdf format). This file need to include the \textit{isf\_draft} variable. 588 A positive value will mean ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh. 589 The exact shape of the ice shelf cavity (grounding line position and minimum thickness of the water column under an ice shelf, ...) can be specify in \nam{zgr_isf}{zgr\_isf}. 590 591 \begin{listing} 592 \caption{\forcode{&namzgr_isf}} 593 \label{lst:namzgr_isf} 594 \begin{forlines} 595 !----------------------------------------------------------------------- 596 &namzgr_isf ! isf cavity geometry definition (default: OFF) 597 !----------------------------------------------------------------------- 598 rn_isfdep_min = 10. ! minimum isf draft tickness (if lower, isf draft set to this value) 599 rn_glhw_min = 1.e-3 ! minimum water column thickness to define the grounding line 600 rn_isfhw_min = 10 ! minimum water column thickness in the cavity once the grounding line defined. 601 ln_isfchannel = .false. ! remove channel (based on 2d mask build from isfdraft-bathy) 602 ln_isfconnect = .false. ! force connection under the ice shelf (based on 2d mask build from isfdraft-bathy) 603 nn_kisfmax = 999 ! limiter in level on the previous condition. (if change larger than this number, get back to value before we enforce the connection) 604 rn_zisfmax = 7000. ! limiter in m on the previous condition. (if change larger than this number, get back to value before we enforce the connection) 605 ln_isfcheminey = .false. ! close cheminey 606 ln_isfsubgl = .false. ! remove subglacial lake created by the remapping process 607 rn_isfsubgllon = 0.0 ! longitude of the seed to determine the open ocean 608 rn_isfsubgllat = 0.0 ! latitude of the seed to determine the open ocean 609 / 610 \end{forlines} 611 \end{listing} 612 613 The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr\_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}). 614 615 \subsection{Model ice shelf draft definition} 616 \label{subsec:zgrisf_isfd} 617 618 First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. 619 There are 3 compulsory steps to achieve this: 620 621 \begin{description} 622 \item{\np{rn_isfdep_min}{rn\_isfdep\_min}:} this is the minimum ice shelf draft. This is to make sure there is no ridiculous thin ice shelf. If \np{rn_isfdep_min}{rn\_isfdep\_min} is smaller than the surface level, \np{rn_isfdep_min}{rn\_isfdep\_min} is set to $e3t\_1d(1)$. 623 Where $h_{isf} < MAX(e3t\_1d(1),rn\_isfdep\_min)$, $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. 624 625 \item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 626 Where the difference between the bathymetry and the ice shelf draft is smaller than \np{rn_glhw_min}{rn\_glhw\_min}, the cell are grounded (ie masked). 627 This step is needed to take into account possible small mismatch between ice shelf draft value and bathymetry value (sources are coming from different grid, different data processes, rounding error, ...). 628 629 \item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity. 630 Where the water column thickness is lower than \np{rn_isfhw_min}{rn\_isfhw\_min}, the ice shelf draft is adjusted to match this criterion. 631 If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. 632 \end{description} 633 634 Once all these adjustements are made, if the water column thickness contains one cell wide channels, these channels can be closed using \np{ln_isfchannel}{ln\_isfchannel}. 635 636 \subsection{Model top level definition} 637 After the definition of the ice shelf draft, the tool defines the top level. 638 The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. 639 To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ 640 641 The process is the following: 642 \begin{description} 643 \item{step 1:} The top level is defined in the same way as the bottom level is defined. 644 \item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) 645 \item{step 3:} The tools make sure, the top level is above or equal to the bottom level 646 \item{step 4:} If the water column at a U- or V- point is one wet cell wide, the ice shelf draft is adjusted. So the actual top cell become fully open and the new 647 top cell thickness is set to the minimum cell thickness allowed (following the same logic as for the bottom partial cell). This step is iterated 4 times to ensure the condition is fullfill along the 4 sides of the cell. 648 \end{description} 649 650 In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft). 651 The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 652 Some limiters in meter or levels on the digging allowed by the tool are available (respectively, \np{rn_zisfmax}{rn\_zisfmax} or \np{rn_kisfmax}{rn\_kisfmax}). 653 This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. 654 655 \subsection{Subglacial lakes} 656 Despite careful setting of your ice shelf draft and bathymetry input file as well as setting described in \autoref{subsec:zgrisf_isfd}, some situation are unavoidable. 657 For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling, 658 you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded). 659 If you do so, the subglacial lakes will show up (Vostock for example). An other possibility is with coarse vertical resolution, some ice shelves could be cut in 2 parts: 660 one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ 661 662 The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. 663 This may be useful for esthetical reason or for stability reasons: 664 665 \begin{description} 666 \item $\bullet$ In a subglacial lakes, in case of very weak circulation (often the case), the only heat flux is the conductive heat flux through the ice sheet. 667 This will lead to constant freezing until water reaches -20C. 668 This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). 669 \item $\bullet$ In case of coupling with an ice sheet model, 670 the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example), 671 and so if for any reason both a connected at some point, the model is likely to fall over.\\ 672 \end{description} 673 674 \section{Closed sea definition} 675 \label{sec:clocfg} 676 677 \begin{listing} 678 \caption{\forcode{&namclo}} 679 \label{lst:namdom_clo} 680 \begin{forlines} 681 !----------------------------------------------------------------------- 682 &namclo ! (closed sea : need ln_domclo = .true. in namcfg) 683 !----------------------------------------------------------------------- 684 rn_lon_opnsea = -2.0 ! longitude seed of open ocean 685 rn_lat_opnsea = -2.0 ! latitude seed of open ocean 686 nn_closea = 8 ! number of closed seas ( = 0; only the open_sea mask will be computed) 687 ! name ! lon_src ! lat_src ! lon_trg ! lat_trg ! river mouth area ! net evap/precip correction scheme ! radius tgt ! id trg 688 ! ! (degree)! (degree)! (degree)! (degree)! local/coast/global ! (glo/rnf/emp) ! (m) ! 689 ! North American lakes 690 sn_lake(1) = 'superior' , -86.57 , 47.30 , -66.49 , 50.45 , 'local' , 'rnf' , 550000.0 , 2 691 sn_lake(2) = 'michigan' , -87.06 , 42.74 , -66.49 , 50.45 , 'local' , 'rnf' , 550000.0 , 2 692 sn_lake(3) = 'huron' , -82.51 , 44.74 , -66.49 , 50.45 , 'local' , 'rnf' , 550000.0 , 2 693 sn_lake(4) = 'erie' , -81.13 , 42.25 , -66.49 , 50.45 , 'local' , 'rnf' , 550000.0 , 2 694 sn_lake(5) = 'ontario' , -77.72 , 43.62 , -66.49 , 50.45 , 'local' , 'rnf' , 550000.0 , 2 695 ! African Lake 696 sn_lake(6) = 'victoria' , 32.93 , -1.08 , 30.44 , 31.37 , 'coast' , 'emp' , 100000.0 , 3 697 ! Asian Lakes 698 sn_lake(7) = 'caspian' , 50.0 , 44.0 , 0.0 , 0.0 , 'global' , 'glo' , 0.0 , 1 699 sn_lake(8) = 'aral' , 60.0 , 45.0 , 0.0 , 0.0 , 'global' , 'glo' , 0.0 , 1 700 / 701 \end{forlines} 702 \end{listing} 703 704 The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{dom_clo}{dom\_clo} (\texttt{DOMAINcfg} only). 705 The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to define:\\ 706 \begin{description} 707 \item $\bullet$ the name of the closed sea (print output purposes). 708 \item $\bullet$ the seed location to define the area of the closed sea (if seed on land because not present in this configuration, this closed sea will be ignored).\\ 709 \item $\bullet$ the seed location for the target area. 710 \item $\bullet$ the type of target area ('local','coast' or 'global'). See point 6 for definition of these cases. 711 \item $\bullet$ the type of redistribution scheme for the net fresh water flux over the closed sea (as a runoff in a target area, as emp in a target area, as emp globally). For the runoff case, if the net fwf is negative, it will be redistribut globally. 712 \item $\bullet$ the radius of the target area (not used for the 'global' case). So the target defined by a 'local' target area of a radius of 100km, for example, correspond to all the wet points within this radius. The coastal case will return only the coastal point within the specifid radius. 713 \item $\bullet$ the target id. This target id is used to group multiple lakes into the same river ouflow (Great Lakes for example). 714 \end{description} 715 716 The closed sea module defines a number of masks in the \textit{domain\_cfg} output: 717 \begin{description} 718 \item[\textit{mask\_opensea}:] a mask of the main ocean without all the closed seas closed. This mask is defined by a flood filling algorithm with an initial seed (localisation defined by \np{rn_lon_opnsea}{rn\_lon\_opnsea} and \np{rn_lat_opnsea}{rn\_lat\_opnsea}). 719 \item[\textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}:] a mask of all the closed seas defined in the namelist by \np{sn_lake}{sn\_lake} for each redistribution scheme. The total number of defined closed seas has to be defined in \np{nn_closea}{nn\_closea}. 720 \item[\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}:] a mask of all the closed seas and targets grouped by target id for each type of redistribution scheme. 721 \item[\textit{mask\_csundef}:] a mask of all the closed sea not defined in \np{sn_lake}{sn\_lake}. This will allows NEMO to mask them if needed or to inform the user of potential minor issues in its bathymetry. 722 \end{description} 723 594 724 \subinc{\input{../../global/epilogue}} 595 725
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