\relax \citation{wal07} \@writefile{toc}{\contentsline {chapter}{\numberline {3}Model Setup}{5}{chapter.3}} \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} \newlabel{cha:setup}{{3}{5}{Model Setup\label {cha:setup}\relax }{chapter.3}{}} \newlabel{sec:setup_region}{{3.1}{5}{The top-level region directory\label {sec:setup_region}\relax }{section.3.1}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.1}The top-level region directory}{5}{section.3.1}} \newlabel{verb:exdirlist}{{3.1}{5}{The top-level region directory\label {sec:setup_region}\relax }{section.3.1}{}} \newlabel{sec:setup_newregion}{{3.1.1}{6}{Setting up a new region\label {sec:setup_newregion}\relax }{subsection.3.1.1}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.1.1}Setting up a new region}{6}{subsection.3.1.1}} \newlabel{sec:setup_topo}{{3.2}{6}{Topography\label {sec:setup_topo}\relax }{section.3.2}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.2}Topography}{6}{section.3.2}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.2.1}Importing a model topography}{7}{subsection.3.2.1}} \newlabel{sec:topo_create}{{3.2.2}{8}{Create a nested model topography \label {sec:topo_create}\relax }{subsection.3.2.2}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.2.2}Create a nested model topography }{8}{subsection.3.2.2}} \newlabel{sec:toporoutines}{{3.2.3}{8}{Help routines for setting up topo-files\label {sec:toporoutines}\relax }{subsection.3.2.3}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.2.3}Help routines for setting up topo-files}{8}{subsection.3.2.3}} \citation{xxx} \@writefile{lot}{\contentsline {table}{\numberline {3.1}{\ignorespaces Environment variables set by the file {\bf EXPT.src}. These are used by most scripts which set up HYCOM. \relax }}{9}{table.caption.2}} \providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}} \newlabel{tab:envvar}{{3.1}{9}{\label {tab:envvar} Environment variables set by the file \file {EXPT.src}. These are used by most scripts which set up HYCOM. \relax \relax }{table.caption.2}{}} \newlabel{sec:setup_expt}{{3.3}{9}{The experiment directories\label {sec:setup_expt}\relax }{section.3.3}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.3}The experiment directories}{9}{section.3.3}} \newlabel{sec:setup_exp}{{3.3.1}{9}{Setting up experiments\label {sec:setup_exp}\relax }{subsection.3.3.1}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.1}Setting up experiments}{9}{subsection.3.3.1}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.2}When to set up new experiments}{10}{subsection.3.3.2}} \@writefile{lot}{\contentsline {table}{\numberline {3.2}{\ignorespaces The bare minimum of variables to set in the file at this stage {\bf blkdat.input}\relax }}{11}{table.caption.3}} \newlabel{tab:blkdat_basic}{{3.2}{11}{\label {tab:blkdat_basic} The bare minimum of variables to set in the file at this stage \file {blkdat.input}\relax \relax }{table.caption.3}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.3}How to create/copy and backup experiment}{11}{subsection.3.3.3}} \newlabel{fig:partita}{{3.1a}{12}{Subfigure 3 3.1a\relax }{subfigure.3.1.1}{}} \newlabel{sub@fig:partita}{{(a)}{a}{Subfigure 3 3.1a\relax }{subfigure.3.1.1}{}} \newlabel{fig:partitb}{{3.1b}{12}{Subfigure 3 3.1b\relax }{subfigure.3.1.2}{}} \newlabel{sub@fig:partitb}{{(b)}{b}{Subfigure 3 3.1b\relax }{subfigure.3.1.2}{}} \@writefile{lof}{\contentsline {figure}{\numberline {3.1}{\ignorespaces Examples of two different MPI partitions of a model domain\relax }}{12}{figure.caption.4}} \@writefile{lof}{\contentsline {subfigure}{\numberline{(a)}{\ignorespaces {Uniform partitioning of domain}}}{12}{subfigure.1.1}} \@writefile{lof}{\contentsline {subfigure}{\numberline{(b)}{\ignorespaces {Non-uniform partitioning of domain}}}{12}{subfigure.1.2}} \newlabel{fig:partit}{{3.1}{12}{Examples of two different MPI partitions of a model domain\relax \relax }{figure.caption.4}{}} \newlabel{sec:setup_partit}{{3.3.4}{12}{Generating MPI partitions \label {sec:setup_partit}\relax }{subsection.3.3.4}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.4}Generating MPI partitions }{12}{subsection.3.3.4}} \newlabel{sec:port}{{3.3.5}{13}{Precribed barotropic inflow: ports.input \label {sec:port}\relax }{subsection.3.3.5}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.5}Precribed barotropic inflow: ports.input }{13}{subsection.3.3.5}} \newlabel{sec:code_cpp}{{3.3.5}{13}{Precribed barotropic inflow: ports.input \label {sec:port}\relax }{subsection.3.3.5}{}} \newlabel{sec:setup_relax}{{3.4}{13}{Relaxation\label {sec:setup_relax}\relax }{section.3.4}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.4}Relaxation}{13}{section.3.4}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.4.1}Routines for generating relaxation fields}{14}{subsection.3.4.1}} \newlabel{fig:rmu}{{\caption@xref {fig:rmu}{ on input line 515}}{15}{Routines for generating relaxation fields\relax }{subfigure.3.2.1}{}} \@writefile{lof}{\contentsline {subfigure}{\numberline{(a)}{\ignorespaces {Example of relaxation mask with the given example of rmu.in. Red areas are equal to 1/20.}}}{15}{subfigure.2.1}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.4.2}Prerequisites for generating relaxation fields}{16}{subsection.3.4.2}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.4.3}Procedure for generating relaxation fields}{16}{subsection.3.4.3}} \newlabel{sec:setup_force}{{3.5}{16}{Forcing\label {sec:setup_force}\relax }{section.3.5}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.5}Forcing}{16}{section.3.5}} \@writefile{lot}{\contentsline {table}{\numberline {3.3}{\ignorespaces Some of the environment variables set by the file {\bf REGION.src} related to forcing datasets.\relax }}{17}{table.caption.6}} \newlabel{tab:forcing_envvar}{{3.3}{17}{\label {tab:forcing_envvar} Some of the environment variables set by the file \file {REGION.src} related to forcing datasets.\relax \relax }{table.caption.6}{}} \@writefile{toc}{\contentsline {subsection}{\numberline {3.5.1}Prerequisites for generating forcing fields}{17}{subsection.3.5.1}} \newlabel{sec:setup_nest}{{3.6}{17}{Nesting setup (subdirectory nest\_nersc)\label {sec:setup_nest}\relax }{section.3.6}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.6}Nesting setup (subdirectory nest\_nersc)}{17}{section.3.6}} \newlabel{sec:port}{{3.6}{18}{Nesting setup (subdirectory nest\_nersc)\label {sec:setup_nest}\relax }{section.3.6}{}} \newlabel{sec:setup_tide}{{3.7}{18}{Tide setup (subdirectory tides\_nersc)\label {sec:setup_tide}\relax }{section.3.7}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.7}Tide setup (subdirectory tides\_nersc)}{18}{section.3.7}} \newlabel{sec:setup_div}{{3.8}{18}{Other setup routines (subdirectory other\_nersc)\label {sec:setup_div}\relax }{section.3.8}{}} \@writefile{toc}{\contentsline {section}{\numberline {3.8}Other setup routines (subdirectory other\_nersc)}{18}{section.3.8}} \@setckpt{inputs/model_setup}{ \setcounter{page}{19} \setcounter{equation}{0} \setcounter{enumi}{3} \setcounter{enumii}{0} \setcounter{enumiii}{0} \setcounter{enumiv}{0} \setcounter{footnote}{1} \setcounter{mpfootnote}{0} \setcounter{part}{0} \setcounter{chapter}{3} \setcounter{section}{8} \setcounter{subsection}{0} \setcounter{subsubsection}{0} \setcounter{paragraph}{0} \setcounter{subparagraph}{0} \setcounter{figure}{1} \setcounter{table}{3} \setcounter{parentequation}{0} \setcounter{NAT@ctr}{0} \setcounter{float@type}{4} \setcounter{Item}{12} \setcounter{Hfootnote}{1} \setcounter{ContinuedFloat}{0} \setcounter{KVtest}{0} \setcounter{subfigure}{0} \setcounter{subfigure@save}{1} \setcounter{lofdepth}{1} \setcounter{subtable}{0} \setcounter{subtable@save}{0} \setcounter{lotdepth}{1} \setcounter{section@level}{1} }