# Changeset 14399

Ignore:
Timestamp:
2021-02-04T19:43:16+01:00 (4 months ago)
Message:

ticket #2581: update branch to head of the trunk

Location:
NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket
Files:
21 edited
1 copied

Unmodified
Removed
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/.svnignore

 r14257 *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/build

• Property svn:ignore
•  old *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/main/bibliography.bib

• Property svn:eol-style set to native
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/main/settings.tex

 r14257 \def\spcup{\vspace*{2.15cm}} \def\hdg{NEMO ocean engine} %\def\shdg{} \def\spcdn{\vspace*{1cm}} \def\autwd{0.25\linewidth} \def\lnlg{270pt} \def\abswd{0.65\linewidth} %\def\shdg{} %% No subheading \def\spcdn{\vspace*{1.00cm}} \def\autwd{0.25\linewidth}\def\lnlg{270pt}\def\abswd{0.65\linewidth} %% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) \def\clr{1,.60,0,.4} \def\clr{1.0,0.6,0.0,0.4} %% IPSL publication number
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/subfiles

• Property svn:ignore
•  old *.aux *.bbl *.blg *.fdb* *.fls *.idx *.ilg *.ind *.ilg *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv cache*
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

 r14303 \label{apdx:DOMCFG} %    {\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 }  \\ \chaptertoc {\footnotesize \begin{tabularx}{\textwidth}{l||X|X} Release & Author(s) & Modifications \\ \hline {\em   next}& {\em Pierre Mathiot} & {\em add ice shelf and closed sea option description } \\ {\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 }  \\ {\em   3.6} & {\em ...} & {\em ...} \\ {\em   3.4} & {\em ...} & {\em ...} \\ {\em <=3.4} & {\em ...} & {\em ...} Release     & Author(s)            & Modifications                                                 \\ \hline {\em  next} & {\em Pierre Mathiot} & {\em Add ice shelf and closed sea option description        } \\ {\em   4.0} & {\em  Andrew Coward} & {\em Creation from materials removed from \autoref{chap:DOM} that are still relevant to the DOMAINcfg tool when setting up new domains                            } \end{tabularx} } the \textit{isfdraft\_meter} file (Netcdf format). This file need to include the \textit{isf\_draft} variable. A positive value will mean ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh. 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}. 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}. \begin{listing} \end{listing} 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}). \subsection{Model ice shelf draft definition} \label{subsec:zgrisf_isfd} First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. There are 3 compulsory steps to achieve this: \begin{description} \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 $e3t\_1d(1)$. Where $h_{isf} < MAX(e3t\_1d(1),\np{rn_isfdep_min}{rn\_isfdep\_min}$), $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. \item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 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). 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, ...). \item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity. 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. If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. \end{description} 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}. 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}). \subsection{Model ice shelf draft definition} \label{subsec:zgrisf_isfd} First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. There are 3 compulsory steps to achieve this: \begin{description} \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 $e3t\_1d(1)$. Where $h_{isf} < MAX(e3t\_1d(1),rn\_isfdep\_min)$, $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. \item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 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). 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, ...). \item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity. 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. If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. \end{description} 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}. \subsection{Model top level definition} After the definition of the ice shelf draft, the tool defines the top level. The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ The process is the following: \begin{description} \item{step 1:} The top level is defined in the same way as the bottom level is defined. \item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) \item{step 3:} The tools make sure, the top level is above or equal to the bottom level \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 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. \end{description} In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft). The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 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}). This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. \subsection{Subglacial lakes} 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. For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling, you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded). 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: one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. This may be useful for esthetical reason or for stability reasons: \begin{description} \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. This will lead to constant freezing until water reaches -20C. This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). \item $\bullet$ In case of coupling with an ice sheet model, the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example), and so if for any reason both a connected at some point, the model is likely to fall over.\\ \end{description} \subsection{Model top level definition} After the definition of the ice shelf draft, the tool defines the top level. The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ The process is the following: \begin{description} \item{step 1:} The top level is defined in the same way as the bottom level is defined. \item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) \item{step 3:} The tools make sure, the top level is above or equal to the bottom level \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 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. \end{description} In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft). The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 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}). This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. \subsection{Subglacial lakes} 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. For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling, you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded). 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: one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. This may be useful for esthetical reason or for stability reasons: \begin{description} \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. This will lead to constant freezing until water reaches -20C. This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). \item $\bullet$ In case of coupling with an ice sheet model, the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example), and so if for any reason both a connected at some point, the model is likely to fall over.\\ \end{description} \section{Closed sea definition} \end{listing} 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{clo}{dom_clo} (\texttt{DOMAINcfg} only). 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). The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to define:\\ \begin{description}
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/subfiles/chap_SBC.tex

 r14303 %% ================================================================================================= \section[Ice Shelf (ISF)]{Interaction with ice shelves (ISF)} \label{sec:isf} \label{sec:SBC_isf} \begin{listing}
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/NEMO/subfiles/chap_TRA.tex

 r14303 (see \autoref{sec:SBC_rnf} for further detail of how it acts on temperature and salinity tendencies) \item [\textit{fwfisf}] The mass flux associated with ice shelf melt, (see \autoref{sec:isf} for further details on how the ice shelf melt is computed and applied). (see \autoref{sec:SBC_isf} for further details on how the ice shelf melt is computed and applied). \end{labeling}
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/SI3/build

• Property svn:ignore
•  old *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/SI3/main/bibliography.bib

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• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/SI3/main/settings.tex

 r11591 %% Engine (folder name) \def \engine{SI3} %% Engine \def\eng{SI3} %% Title and cover page settings \def \spacetop{  \vspace*{1.2cm} } \def \heading{Sea Ice modelling Integrated Initiative (SI$^3$)} \def \subheading{The NEMO sea ice engine} \def \spacedown{ \vspace*{  1cm} } \def \authorswidth{0.2\linewidth} \def \rulelenght{230pt} \def \abstractwidth{0.65\linewidth} %% Cover page \def\spcup{\vspace*{1.20cm}} \def \hdg{Sea Ice modelling Integrated Initiative (SI$^3$)} \def\shdg{The NEMO sea ice engine                         } \def\spcdn{\vspace*{1.00cm}} \def\autwd{0.20\linewidth}\def\lnlg{230pt}\def\abswd{0.65\linewidth} %% Color for document (frontpage banner, links and chapter boxes) \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} } %% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) \def\clr{0.0,0.0,0.0,0.4} %% IPSL publication number \def \ipslnum{31} \def\ipsl{31} %% Zenodo ID, i.e. doi:10.5281/zenodo.$$[0-9]*$$ \def \zid{1471689} %% Zenodo ID, i.e. doi:10.5281/zenodo.\zid \def\zid{1471689}
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/SI3/subfiles

• Property svn:ignore
•  old *.aux *.bbl *.blg *.fdb* *.fls *.idx *.ilg *.ind *.ilg *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv cache*
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/TOP/build

• Property svn:ignore
•  old *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/TOP/main/bibliography.bib

• Property svn:eol-style set to native
 r11171 journal   = {Global Biogeochemical Cycles}, publisher = {American Geophysical Union (AGU)} } @techreport{      gibson_trpt86, title         = "Standards for software development and maintenance", pages         = "21", series        = "ECMWF Technical Memoranda", number        = "120", author        = "J. K. Gibson", institution   = "ECMWF Operations Department; Reading, United Kingdom", year          = "1986", month         = "aug", doi           = "10.21957/gi113q4gn" }
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/TOP/main/settings.tex

 r11591 %% Engine (folder name) \def \engine{TOP} %% Engine \def\eng{TOP} %% Title and cover page settings \def \spacetop{  \vspace*{1.3cm} } \def \heading{Tracers in Ocean Paradigm (TOP)} \def \subheading{The NEMO passive tracers engine} \def \spacedown{ \vspace*{  1cm} } \def \authorswidth{0.15\linewidth} \def \rulelenght{110pt} \def \abstractwidth{0.7\linewidth} %% Cover page \def\spcup{\vspace*{1.30cm}} \def \hdg{Tracers in Ocean Paradigm (TOP)} \def\shdg{The NEMO passive tracers engine} \def\spcdn{\vspace*{1.00cm}} \def\autwd{0.15\linewidth}\def\lnlg{110pt}\def\abswd{0.70\linewidth} %% Color for document (frontpage banner, links and chapter boxes) \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, .4} } %% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) \def\clr{1.0,0.0,1.0,0.4} %% IPSL publication number \def \ipslnum{28} \def\ipsl{28} %% Zenodo ID, i.e. doi:10.5281/zenodo.$$[0-9]*$$ \def \zid{1471700} %% Zenodo ID, i.e. doi:10.5281/zenodo.\zid \def\zid{1471700}
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/TOP/subfiles

• Property svn:ignore
•  old *.aux *.bbl *.blg *.fdb* *.fls *.idx *.ilg *.ind *.lo* *.out *.pdf *.pyg *.tdo *.toc *.xdv cache*
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/TOP/subfiles/model_description.tex

• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/doc/latex/global/latexmk.pl

 r14257 ## Custom cmds set_tex_cmds('-shell-escape -interaction=batchmode'); #set_tex_cmds('-shell-escape'); $makeindex = 'makeindex -s %R.ist %O -o %D %S'; set_tex_cmds('-shell-escape -file-line-error -interaction=batchmode'); #set_tex_cmds('-shell-escape -file-line-error');$makeindex = 'makeindex %O -s %R.ist -o %D %S'; ## %D: Destination file (.ind for index) ## %O: Options ## %R: Root filename (\${model}_manual) ## %S: Source file      (.idx for index)
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/src/OCE/SBC/sbcblk.F90

 r14072 !                                      !- fill the bulk structure with namelist informations CALL fld_fill( sf, slf_i, cn_dir, 'sbc_blk_init', 'surface boundary condition -- bulk formulae', 'namsbc_blk' ) sf(jp_wndi )%zsgn = -1._wp   ;   sf(jp_wndj )%zsgn = -1._wp   ! vector field at T point: overwrite default definition of zsgn sf(jp_uoatm)%zsgn = -1._wp   ;   sf(jp_uoatm)%zsgn = -1._wp   ! vector field at T point: overwrite default definition of zsgn sf(jp_hpgi )%zsgn = -1._wp   ;   sf(jp_hpgj )%zsgn = -1._wp   ! vector field at T point: overwrite default definition of zsgn ! DO jfpr= 1, jpfld
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/src/OCE/SBC/sbcflx.F90

 r14072 !                                         ! fill sf with slf_i and control print CALL fld_fill( sf, slf_i, cn_dir, 'sbc_flx', 'flux formulation for ocean surface boundary condition', 'namsbc_flx' ) sf(jp_utau)%cltype = 'U'   ;   sf(jp_utau)%zsgn = -1._wp   ! vector field at U point: overwrite default definition of cltype and zsgn sf(jp_vtau)%cltype = 'V'   ;   sf(jp_vtau)%zsgn = -1._wp   ! vector field at V point: overwrite default definition of cltype and zsgn ! ENDIF !!clem: I do not think it is needed !!qns(:,:) = qns(:,:) - emp(:,:) * sst_m(:,:) * rcp        ! mass flux is at SST ! ! clem: without these lbc calls, it seems that the northfold is not ok (true in 3.6, not sure in 4.x) CALL lbc_lnk_multi( 'sbcflx', utau, 'U', -1._wp, vtau, 'V', -1._wp, & &                           qns, 'T',  1._wp, emp , 'T',  1._wp, qsr, 'T', 1._wp ) !! sfx, 'T', 1._wp  ) ! IF( nitend-nit000 <= 100 .AND. lwp ) THEN                ! control print (if less than 100 time-step asked)
• ## NEMO/branches/2021/ticket2581_trunk_icb_speeding_ticket/src/OCE/SBC/sbcwave.F90

 r14072 ! CALL fld_fill( sf_sd, slf_i, cn_dir, 'sbc_wave_init', 'Wave module ', 'namsbc_wave' ) sf_sd(jp_usd)%zsgn = -1._wp   ;  sf_sd(jp_vsd)%zsgn = -1._wp   ! vector field at T point: overwrite default definition of zsgn ENDIF !
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