| 79 |
|
|
| 80 |
\end{enumerate} |
\end{enumerate} |
| 81 |
|
|
| 82 |
|
\subsubsection{Checkout from CVS} |
| 83 |
|
\label{sect:cvs_checkout} |
| 84 |
|
|
| 85 |
If CVS is available on your system, we strongly encourage you to use it. CVS |
If CVS is available on your system, we strongly encourage you to use it. CVS |
| 86 |
provides an efficient and elegant way of organizing your code and keeping |
provides an efficient and elegant way of organizing your code and keeping |
| 87 |
track of your changes. If CVS is not available on your machine, you can also |
track of your changes. If CVS is not available on your machine, you can also |
| 96 |
\begin{verbatim} |
\begin{verbatim} |
| 97 |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
| 98 |
\end{verbatim} |
\end{verbatim} |
| 99 |
in your .profile or .bashrc file. |
in your \texttt{.profile} or \texttt{.bashrc} file. |
| 100 |
|
|
| 101 |
|
|
| 102 |
To get MITgcm through CVS, first register with the MITgcm CVS server |
To get MITgcm through CVS, first register with the MITgcm CVS server |
| 124 |
\end{verbatim} |
\end{verbatim} |
| 125 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 126 |
|
|
| 127 |
|
As a convenience, the MITgcm CVS server contains aliases which are |
| 128 |
|
named subsets of the codebase. These aliases can be especially |
| 129 |
|
helpful when used over slow internet connections or on machines with |
| 130 |
|
restricted storage space. Table \ref{tab:cvsModules} contains a list |
| 131 |
|
of CVS aliases |
| 132 |
|
\begin{table}[htb] |
| 133 |
|
\centering |
| 134 |
|
\begin{tabular}[htb]{|lp{3.25in}|}\hline |
| 135 |
|
\textbf{Alias Name} & \textbf{Information (directories) Contained} \\\hline |
| 136 |
|
\texttt{MITgcm\_code} & Only the source code -- none of the verification examples. \\ |
| 137 |
|
\texttt{MITgcm\_verif\_basic} |
| 138 |
|
& Source code plus a small set of the verification examples |
| 139 |
|
(\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, |
| 140 |
|
\texttt{front\_relax}, and \texttt{plume\_on\_slope}). \\ |
| 141 |
|
\texttt{MITgcm\_verif\_atmos} & Source code plus all of the atmospheric examples. \\ |
| 142 |
|
\texttt{MITgcm\_verif\_ocean} & Source code plus all of the oceanic examples. \\ |
| 143 |
|
\texttt{MITgcm\_verif\_all} & Source code plus all of the |
| 144 |
|
verification examples. \\\hline |
| 145 |
|
\end{tabular} |
| 146 |
|
\caption{MITgcm CVS Modules} |
| 147 |
|
\label{tab:cvsModules} |
| 148 |
|
\end{table} |
| 149 |
|
|
| 150 |
The checkout process creates a directory called \textit{MITgcm}. If |
The checkout process creates a directory called \textit{MITgcm}. If |
| 151 |
the directory \textit{MITgcm} exists this command updates your code |
the directory \textit{MITgcm} exists this command updates your code |
| 159 |
here |
here |
| 160 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 161 |
. |
. |
| 162 |
|
It is important to note that the CVS aliases in Table |
| 163 |
|
\ref{tab:cvsModules} cannot be used in conjunction with the CVS |
| 164 |
|
\texttt{-d DIRNAME} option. However, the \texttt{MITgcm} directories |
| 165 |
|
they create can be changed to a different name following the check-out: |
| 166 |
|
\begin{verbatim} |
| 167 |
|
% cvs co MITgcm_verif_basic |
| 168 |
|
% mv MITgcm MITgcm_verif_basic |
| 169 |
|
\end{verbatim} |
| 170 |
|
|
| 171 |
|
|
| 172 |
\paragraph*{Conventional download method} |
\subsubsection{Conventional download method} |
| 173 |
\label{sect:conventionalDownload} |
\label{sect:conventionalDownload} |
| 174 |
|
|
| 175 |
If you do not have CVS on your system, you can download the model as a |
If you do not have CVS on your system, you can download the model as a |
| 189 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 190 |
mailing list. |
mailing list. |
| 191 |
|
|
| 192 |
\paragraph*{Upgrading from an earlier version} |
\subsubsection{Upgrading from an earlier version} |
| 193 |
|
|
| 194 |
If you already have an earlier version of the code you can ``upgrade'' |
If you already have an earlier version of the code you can ``upgrade'' |
| 195 |
your copy instead of downloading the entire repository again. First, |
your copy instead of downloading the entire repository again. First, |
| 324 |
|
|
| 325 |
\end{itemize} |
\end{itemize} |
| 326 |
|
|
| 327 |
\section{Example experiments} |
\section[MITgcm Example Experiments]{Example experiments} |
| 328 |
\label{sect:modelExamples} |
\label{sect:modelExamples} |
| 329 |
|
|
| 330 |
%% a set of twenty-four pre-configured numerical experiments |
%% a set of twenty-four pre-configured numerical experiments |
| 484 |
Once you have chosen the example you want to run, you are ready to |
Once you have chosen the example you want to run, you are ready to |
| 485 |
compile the code. |
compile the code. |
| 486 |
|
|
| 487 |
\section{Building the code} |
\section[Building MITgcm]{Building the code} |
| 488 |
\label{sect:buildingCode} |
\label{sect:buildingCode} |
| 489 |
|
|
| 490 |
To compile the code, we use the {\em make} program. This uses a file |
To compile the code, we use the {\em make} program. This uses a file |
| 666 |
\end{verbatim} |
\end{verbatim} |
| 667 |
|
|
| 668 |
|
|
| 669 |
|
\subsection{Using \texttt{genmake2}} |
|
\subsection{Using \textit{genmake2}} |
|
| 670 |
\label{sect:genmake} |
\label{sect:genmake} |
| 671 |
|
|
| 672 |
To compile the code, first use the program \texttt{genmake2} (located |
To compile the code, first use the program \texttt{genmake2} (located |
| 673 |
in the \textit{tools} directory) to generate a Makefile. |
in the \texttt{tools} directory) to generate a Makefile. |
| 674 |
\texttt{genmake2} is a shell script written to work with all |
\texttt{genmake2} is a shell script written to work with all |
| 675 |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
| 676 |
Internally, \texttt{genmake2} determines the locations of needed |
Internally, \texttt{genmake2} determines the locations of needed |
| 677 |
files, the compiler, compiler options, libraries, and Unix tools. It |
files, the compiler, compiler options, libraries, and Unix tools. It |
| 678 |
relies upon a number of ``optfiles'' located in the {\em |
relies upon a number of ``optfiles'' located in the |
| 679 |
tools/build\_options} directory. |
\texttt{tools/build\_options} directory. |
| 680 |
|
|
| 681 |
The purpose of the optfiles is to provide all the compilation options |
The purpose of the optfiles is to provide all the compilation options |
| 682 |
for particular ``platforms'' (where ``platform'' roughly means the |
for particular ``platforms'' (where ``platform'' roughly means the |
| 771 |
the user's path. When these three items have been identified, |
the user's path. When these three items have been identified, |
| 772 |
genmake2 will try to find an optfile that has a matching name. |
genmake2 will try to find an optfile that has a matching name. |
| 773 |
|
|
| 774 |
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
| 775 |
|
set of packages to be used. The normal order of precedence for |
| 776 |
|
packages is as follows: |
| 777 |
|
\begin{enumerate} |
| 778 |
|
\item If available, the command line (\texttt{--pdefault}) settings |
| 779 |
|
over-rule any others. |
| 780 |
|
|
| 781 |
|
\item Next, \texttt{genmake2} will look for a file named |
| 782 |
|
``\texttt{packages.conf}'' in the local directory or in any of the |
| 783 |
|
directories specified with the \texttt{--mods} option. |
| 784 |
|
|
| 785 |
|
\item Finally, if neither of the above are available, |
| 786 |
|
\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
| 787 |
|
\end{enumerate} |
| 788 |
|
|
| 789 |
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
| 790 |
used for packages. |
used for packages. |
| 791 |
|
|
| 798 |
assumed that the two packages are compatible and will function |
assumed that the two packages are compatible and will function |
| 799 |
either with or without each other. |
either with or without each other. |
| 800 |
|
|
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
|
|
set of packages to be used. |
|
|
|
|
|
If not set, the default package list will be read from {\em |
|
|
pkg/pkg\_default} |
|
|
|
|
| 801 |
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
| 802 |
automatic differentiation options file to be used. The file is |
automatic differentiation options file to be used. The file is |
| 803 |
analogous to the ``optfile'' defined above but it specifies |
analogous to the ``optfile'' defined above but it specifies |
| 827 |
``-standarddirs'' option) |
``-standarddirs'' option) |
| 828 |
\end{itemize} |
\end{itemize} |
| 829 |
|
|
| 830 |
|
\item[\texttt{--mpi}] This option enables certain MPI features (using |
| 831 |
|
CPP \texttt{\#define}s) within the code and is necessary for MPI |
| 832 |
|
builds (see Section \ref{sect:mpi-build}). |
| 833 |
|
|
| 834 |
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
| 835 |
soft-links and other bugs common with the \texttt{make} versions |
soft-links and other bugs common with the \texttt{make} versions |
| 836 |
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
| 837 |
called \texttt{gmake}) should be preferred. This option provides a |
called \texttt{gmake}) should be preferred. This option provides a |
| 838 |
means for specifying the make executable to be used. |
means for specifying the make executable to be used. |
| 839 |
|
|
| 840 |
|
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
| 841 |
|
machines, the ``bash'' shell is unavailable. To run on these |
| 842 |
|
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
| 843 |
|
a Bourne, POSIX, or compatible) shell. The syntax in these |
| 844 |
|
circumstances is: |
| 845 |
|
\begin{center} |
| 846 |
|
\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
| 847 |
|
\end{center} |
| 848 |
|
where \texttt{/bin/sh} can be replaced with the full path and name |
| 849 |
|
of the desired shell. |
| 850 |
|
|
| 851 |
\end{description} |
\end{description} |
| 852 |
|
|
| 853 |
|
|
| 854 |
|
\subsection{Building with MPI} |
| 855 |
|
\label{sect:mpi-build} |
| 856 |
|
|
| 857 |
|
Building MITgcm to use MPI libraries can be complicated due to the |
| 858 |
|
variety of different MPI implementations available, their dependencies |
| 859 |
|
or interactions with different compilers, and their often ad-hoc |
| 860 |
|
locations within file systems. For these reasons, its generally a |
| 861 |
|
good idea to start by finding and reading the documentation for your |
| 862 |
|
machine(s) and, if necessary, seeking help from your local systems |
| 863 |
|
administrator. |
| 864 |
|
|
| 865 |
\section{Running the model} |
The steps for building MITgcm with MPI support are: |
| 866 |
|
\begin{enumerate} |
| 867 |
|
|
| 868 |
|
\item Determine the locations of your MPI-enabled compiler and/or MPI |
| 869 |
|
libraries and put them into an options file as described in Section |
| 870 |
|
\ref{sect:genmake}. One can start with one of the examples in: |
| 871 |
|
\begin{rawhtml} <A |
| 872 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
| 873 |
|
\end{rawhtml} |
| 874 |
|
\begin{center} |
| 875 |
|
\texttt{MITgcm/tools/build\_options/} |
| 876 |
|
\end{center} |
| 877 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 878 |
|
such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
| 879 |
|
\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
| 880 |
|
hand. You may need help from your user guide or local systems |
| 881 |
|
administrator to determine the exact location of the MPI libraries. |
| 882 |
|
If libraries are not installed, MPI implementations and related |
| 883 |
|
tools are available including: |
| 884 |
|
\begin{itemize} |
| 885 |
|
\item \begin{rawhtml} <A |
| 886 |
|
href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
| 887 |
|
\end{rawhtml} |
| 888 |
|
MPICH |
| 889 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 890 |
|
|
| 891 |
|
\item \begin{rawhtml} <A |
| 892 |
|
href="http://www.lam-mpi.org/"> |
| 893 |
|
\end{rawhtml} |
| 894 |
|
LAM/MPI |
| 895 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 896 |
|
|
| 897 |
|
\item \begin{rawhtml} <A |
| 898 |
|
href="http://www.osc.edu/~pw/mpiexec/"> |
| 899 |
|
\end{rawhtml} |
| 900 |
|
MPIexec |
| 901 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 902 |
|
\end{itemize} |
| 903 |
|
|
| 904 |
|
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
| 905 |
|
(see Section \ref{sect:genmake}) using commands such as: |
| 906 |
|
{\footnotesize \begin{verbatim} |
| 907 |
|
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
| 908 |
|
% make depend |
| 909 |
|
% make |
| 910 |
|
\end{verbatim} } |
| 911 |
|
|
| 912 |
|
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
| 913 |
|
program provided with your particular implementation of MPI. |
| 914 |
|
Typical MPI packages such as MPICH will use something like: |
| 915 |
|
\begin{verbatim} |
| 916 |
|
% mpirun -np 4 -machinefile mf ./mitgcmuv |
| 917 |
|
\end{verbatim} |
| 918 |
|
Sightly more complicated scripts may be needed for many machines |
| 919 |
|
since execution of the code may be controlled by both the MPI |
| 920 |
|
library and a job scheduling and queueing system such as PBS, |
| 921 |
|
LoadLeveller, Condor, or any of a number of similar tools. A few |
| 922 |
|
example scripts (those used for our \begin{rawhtml} <A |
| 923 |
|
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
| 924 |
|
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
| 925 |
|
at: |
| 926 |
|
\begin{rawhtml} <A |
| 927 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
| 928 |
|
\end{rawhtml} |
| 929 |
|
{\footnotesize \tt |
| 930 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
| 931 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 932 |
|
|
| 933 |
|
\end{enumerate} |
| 934 |
|
|
| 935 |
|
An example of the above process on the MITgcm cluster (``cg01'') using |
| 936 |
|
the GNU g77 compiler and the mpich MPI library is: |
| 937 |
|
|
| 938 |
|
{\footnotesize \begin{verbatim} |
| 939 |
|
% cd MITgcm/verification/exp5 |
| 940 |
|
% mkdir build |
| 941 |
|
% cd build |
| 942 |
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
| 943 |
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
| 944 |
|
% make depend |
| 945 |
|
% make |
| 946 |
|
% cd ../input |
| 947 |
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
| 948 |
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
| 949 |
|
\end{verbatim} } |
| 950 |
|
|
| 951 |
|
|
| 952 |
|
|
| 953 |
|
\section[Running MITgcm]{Running the model in prognostic mode} |
| 954 |
\label{sect:runModel} |
\label{sect:runModel} |
| 955 |
|
|
| 956 |
If compilation finished succesfuully (section \ref{sect:buildModel}) |
If compilation finished succesfuully (section \ref{sect:buildingCode}) |
| 957 |
then an executable called {\em mitgcmuv} will now exist in the local |
then an executable called \texttt{mitgcmuv} will now exist in the |
| 958 |
directory. |
local directory. |
| 959 |
|
|
| 960 |
To run the model as a single process (ie. not in parallel) simply |
To run the model as a single process (ie. not in parallel) simply |
| 961 |
type: |
type: |
| 1059 |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
| 1060 |
\end{verbatim} |
\end{verbatim} |
| 1061 |
|
|
| 1062 |
\section{Doing it yourself: customizing the code} |
\section[Customizing MITgcm]{Doing it yourself: customizing the code} |
| 1063 |
|
|
| 1064 |
When you are ready to run the model in the configuration you want, the |
When you are ready to run the model in the configuration you want, the |
| 1065 |
easiest thing is to use and adapt the setup of the case studies |
easiest thing is to use and adapt the setup of the case studies |
| 1094 |
\begin{description} |
\begin{description} |
| 1095 |
\item[dimensions] \ |
\item[dimensions] \ |
| 1096 |
|
|
| 1097 |
The number of points in the x, y,\textit{\ }and r\textit{\ |
The number of points in the x, y, and r directions are represented |
| 1098 |
}directions are represented by the variables \textbf{sNx}\textit{, |
by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |
| 1099 |
}\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively |
respectively which are declared and set in the file |
| 1100 |
which are declared and set in the file \textit{model/inc/SIZE.h. |
\textit{model/inc/SIZE.h}. (Again, this assumes a mono-processor |
| 1101 |
}(Again, this assumes a mono-processor calculation. For |
calculation. For multiprocessor calculations see the section on |
| 1102 |
multiprocessor calculations see section on parallel implementation.) |
parallel implementation.) |
| 1103 |
|
|
| 1104 |
\item[grid] \ |
\item[grid] \ |
| 1105 |
|
|
| 1106 |
Three different grids are available: cartesian, spherical polar, and |
Three different grids are available: cartesian, spherical polar, and |
| 1107 |
curvilinear (including the cubed sphere). The grid is set through |
curvilinear (which includes the cubed sphere). The grid is set |
| 1108 |
the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{ |
through the logical variables \textbf{usingCartesianGrid}, |
| 1109 |
usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{ |
\textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |
| 1110 |
usingCurvilinearGrid}\textit{. }In the case of spherical and |
In the case of spherical and curvilinear grids, the southern |
| 1111 |
curvilinear grids, the southern boundary is defined through the |
boundary is defined through the variable \textbf{phiMin} which |
| 1112 |
variable \textbf{phiMin} \textit{\ }which corresponds to the |
corresponds to the latitude of the southern most cell face (in |
| 1113 |
latitude of the southern most cell face (in degrees). The resolution |
degrees). The resolution along the x and y directions is controlled |
| 1114 |
along the x and y directions is controlled by the 1D arrays |
by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the |
| 1115 |
\textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in |
case of a cartesian grid, in degrees otherwise). The vertical grid |
| 1116 |
the case of a cartesian grid, in degrees otherwise). The vertical |
spacing is set through the 1D array \textbf{delz} for the ocean (in |
| 1117 |
grid spacing is set through the 1D array \textbf{delz }for the ocean |
meters) or \textbf{delp} for the atmosphere (in Pa). The variable |
| 1118 |
(in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa). |
\textbf{Ro\_SeaLevel} represents the standard position of Sea-Level |
| 1119 |
The variable \textbf{ Ro\_SeaLevel} represents the standard position |
in ``R'' coordinate. This is typically set to 0m for the ocean |
| 1120 |
of Sea-Level in ''R'' coordinate. This is typically set to 0m for |
(default value) and 10$^{5}$Pa for the atmosphere. For the |
| 1121 |
the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For |
atmosphere, also set the logical variable \textbf{groundAtK1} to |
| 1122 |
the atmosphere, also set the logical variable \textbf{groundAtK1} to |
\texttt{'.TRUE.'} which puts the first level (k=1) at the lower |
|
'.\texttt{TRUE}.'. which put the first level (k=1) at the lower |
|
| 1123 |
boundary (ground). |
boundary (ground). |
| 1124 |
|
|
| 1125 |
For the cartesian grid case, the Coriolis parameter $f$ is set |
For the cartesian grid case, the Coriolis parameter $f$ is set |
| 1126 |
through the variables \textbf{f0}\textit{\ }and |
through the variables \textbf{f0} and \textbf{beta} which correspond |
| 1127 |
\textbf{beta}\textit{\ }which correspond to the reference Coriolis |
to the reference Coriolis parameter (in s$^{-1}$) and |
| 1128 |
parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in |
$\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. |
| 1129 |
m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set |
If \textbf{beta } is set to a nonzero value, \textbf{f0} is the |
| 1130 |
to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the |
value of $f$ at the southern edge of the domain. |
|
southern edge of the domain. |
|
| 1131 |
|
|
| 1132 |
\item[topography - full and partial cells] \ |
\item[topography - full and partial cells] \ |
| 1133 |
|
|
| 1134 |
The domain bathymetry is read from a file that contains a 2D (x,y) |
The domain bathymetry is read from a file that contains a 2D (x,y) |
| 1135 |
map of depths (in m) for the ocean or pressures (in Pa) for the |
map of depths (in m) for the ocean or pressures (in Pa) for the |
| 1136 |
atmosphere. The file name is represented by the variable |
atmosphere. The file name is represented by the variable |
| 1137 |
\textbf{bathyFile}\textit{. }The file is assumed to contain binary |
\textbf{bathyFile}. The file is assumed to contain binary numbers |
| 1138 |
numbers giving the depth (pressure) of the model at each grid cell, |
giving the depth (pressure) of the model at each grid cell, ordered |
| 1139 |
ordered with the x coordinate varying fastest. The points are |
with the x coordinate varying fastest. The points are ordered from |
| 1140 |
ordered from low coordinate to high coordinate for both axes. The |
low coordinate to high coordinate for both axes. The model code |
| 1141 |
model code applies without modification to enclosed, periodic, and |
applies without modification to enclosed, periodic, and double |
| 1142 |
double periodic domains. Periodicity is assumed by default and is |
periodic domains. Periodicity is assumed by default and is |
| 1143 |
suppressed by setting the depths to 0m for the cells at the limits |
suppressed by setting the depths to 0m for the cells at the limits |
| 1144 |
of the computational domain (note: not sure this is the case for the |
of the computational domain (note: not sure this is the case for the |
| 1145 |
atmosphere). The precision with which to read the binary data is |
atmosphere). The precision with which to read the binary data is |
| 1146 |
controlled by the integer variable \textbf{readBinaryPrec }which can |
controlled by the integer variable \textbf{readBinaryPrec} which can |
| 1147 |
take the value \texttt{32} (single precision) or \texttt{64} (double |
take the value \texttt{32} (single precision) or \texttt{64} (double |
| 1148 |
precision). See the matlab program \textit{ gendata.m }in the |
precision). See the matlab program \textit{gendata.m} in the |
| 1149 |
\textit{input }directories under \textit{verification }to see how |
\textit{input} directories under \textit{verification} to see how |
| 1150 |
the bathymetry files are generated for the case study experiments. |
the bathymetry files are generated for the case study experiments. |
| 1151 |
|
|
| 1152 |
To use the partial cell capability, the variable |
To use the partial cell capability, the variable \textbf{hFacMin} |
| 1153 |
\textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and |
needs to be set to a value between 0 and 1 (it is set to 1 by |
| 1154 |
1 (it is set to 1 by default) corresponding to the minimum |
default) corresponding to the minimum fractional size of the cell. |
| 1155 |
fractional size of the cell. For example if the bottom cell is 500m |
For example if the bottom cell is 500m thick and \textbf{hFacMin} is |
| 1156 |
thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual |
set to 0.1, the actual thickness of the cell (i.e. used in the code) |
| 1157 |
thickness of the cell (i.e. used in the code) can cover a range of |
can cover a range of discrete values 50m apart from 50m to 500m |
| 1158 |
discrete values 50m apart from 50m to 500m depending on the value of |
depending on the value of the bottom depth (in \textbf{bathyFile}) |
| 1159 |
the bottom depth (in \textbf{bathyFile}) at this point. |
at this point. |
| 1160 |
|
|
| 1161 |
Note that the bottom depths (or pressures) need not coincide with |
Note that the bottom depths (or pressures) need not coincide with |
| 1162 |
the models levels as deduced from \textbf{delz}\textit{\ |
the models levels as deduced from \textbf{delz} or \textbf{delp}. |
| 1163 |
}or\textit{\ }\textbf{delp} \textit{. }The model will interpolate |
The model will interpolate the numbers in \textbf{bathyFile} so that |
| 1164 |
the numbers in \textbf{bathyFile} \textit{\ }so that they match the |
they match the levels obtained from \textbf{delz} or \textbf{delp} |
| 1165 |
levels obtained from \textbf{delz}\textit{ \ }or\textit{\ |
and \textbf{hFacMin}. |
|
}\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. } |
|
| 1166 |
|
|
| 1167 |
(Note: the atmospheric case is a bit more complicated than what is |
(Note: the atmospheric case is a bit more complicated than what is |
| 1168 |
written here I think. To come soon...) |
written here I think. To come soon...) |
| 1177 |
\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |
\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |
| 1178 |
through the variable \textbf{abEps} (dimensionless). The stagger |
through the variable \textbf{abEps} (dimensionless). The stagger |
| 1179 |
baroclinic time stepping can be activated by setting the logical |
baroclinic time stepping can be activated by setting the logical |
| 1180 |
variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'. |
variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. |
| 1181 |
|
|
| 1182 |
\end{description} |
\end{description} |
| 1183 |
|
|
| 1195 |
|
|
| 1196 |
The form of the equation of state is controlled by the character |
The form of the equation of state is controlled by the character |
| 1197 |
variables \textbf{buoyancyRelation} and \textbf{eosType}. |
variables \textbf{buoyancyRelation} and \textbf{eosType}. |
| 1198 |
\textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and |
\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and |
| 1199 |
needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. |
needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. |
| 1200 |
In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'. |
In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. |
| 1201 |
For the ocean, two forms of the equation of state are available: |
For the ocean, two forms of the equation of state are available: |
| 1202 |
linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial |
linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial |
| 1203 |
approximation to the full nonlinear equation ( set |
approximation to the full nonlinear equation ( set \textbf{eosType} to |
| 1204 |
\textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear |
\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |
| 1205 |
case, you need to specify the thermal and haline expansion |
thermal and haline expansion coefficients represented by the variables |
| 1206 |
coefficients represented by the variables \textbf{tAlpha}\textit{\ |
\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For |
| 1207 |
}(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear |
the nonlinear case, you need to generate a file of polynomial |
| 1208 |
case, you need to generate a file of polynomial coefficients called |
coefficients called \textit{POLY3.COEFFS}. To do this, use the program |
|
\textit{POLY3.COEFFS}. To do this, use the program |
|
| 1209 |
\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |
\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |
| 1210 |
available in the same directory and you will need to edit the number |
available in the same directory and you will need to edit the number |
| 1211 |
and the values of the vertical levels in \textit{knudsen2.f} so that |
and the values of the vertical levels in \textit{knudsen2.f} so that |
| 1213 |
|
|
| 1214 |
There there are also higher polynomials for the equation of state: |
There there are also higher polynomials for the equation of state: |
| 1215 |
\begin{description} |
\begin{description} |
| 1216 |
\item['\texttt{UNESCO}':] The UNESCO equation of state formula of |
\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of |
| 1217 |
Fofonoff and Millard \cite{fofonoff83}. This equation of state |
Fofonoff and Millard \cite{fofonoff83}. This equation of state |
| 1218 |
assumes in-situ temperature, which is not a model variable; \emph{its use |
assumes in-situ temperature, which is not a model variable; {\em its |
| 1219 |
is therefore discouraged, and it is only listed for completeness}. |
use is therefore discouraged, and it is only listed for |
| 1220 |
\item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and |
completeness}. |
| 1221 |
|
\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and |
| 1222 |
McDougall \cite{jackett95}, which uses the model variable potential |
McDougall \cite{jackett95}, which uses the model variable potential |
| 1223 |
temperature as input. The '\texttt{Z}' indicates that this equation |
temperature as input. The \texttt{'Z'} indicates that this equation |
| 1224 |
of state uses a horizontally and temporally constant pressure |
of state uses a horizontally and temporally constant pressure |
| 1225 |
$p_{0}=-g\rho_{0}z$. |
$p_{0}=-g\rho_{0}z$. |
| 1226 |
\item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and |
\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and |
| 1227 |
McDougall \cite{jackett95}, which uses the model variable potential |
McDougall \cite{jackett95}, which uses the model variable potential |
| 1228 |
temperature as input. The '\texttt{P}' indicates that this equation |
temperature as input. The \texttt{'P'} indicates that this equation |
| 1229 |
of state uses the actual hydrostatic pressure of the last time |
of state uses the actual hydrostatic pressure of the last time |
| 1230 |
step. Lagging the pressure in this way requires an additional pickup |
step. Lagging the pressure in this way requires an additional pickup |
| 1231 |
file for restarts. |
file for restarts. |
| 1232 |
\item['\texttt{MDJWF}':] The new, more accurate and less expensive |
\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive |
| 1233 |
equation of state by McDougall et~al. \cite{mcdougall03}. It also |
equation of state by McDougall et~al. \cite{mcdougall03}. It also |
| 1234 |
requires lagging the pressure and therefore an additional pickup |
requires lagging the pressure and therefore an additional pickup |
| 1235 |
file for restarts. |
file for restarts. |
| 1239 |
|
|
| 1240 |
\subsection{Momentum equations} |
\subsection{Momentum equations} |
| 1241 |
|
|
| 1242 |
In this section, we only focus for now on the parameters that you are likely |
In this section, we only focus for now on the parameters that you are |
| 1243 |
to change, i.e. the ones relative to forcing and dissipation for example. |
likely to change, i.e. the ones relative to forcing and dissipation |
| 1244 |
The details relevant to the vector-invariant form of the equations and the |
for example. The details relevant to the vector-invariant form of the |
| 1245 |
various advection schemes are not covered for the moment. We assume that you |
equations and the various advection schemes are not covered for the |
| 1246 |
use the standard form of the momentum equations (i.e. the flux-form) with |
moment. We assume that you use the standard form of the momentum |
| 1247 |
the default advection scheme. Also, there are a few logical variables that |
equations (i.e. the flux-form) with the default advection scheme. |
| 1248 |
allow you to turn on/off various terms in the momentum equation. These |
Also, there are a few logical variables that allow you to turn on/off |
| 1249 |
variables are called \textbf{momViscosity, momAdvection, momForcing, |
various terms in the momentum equation. These variables are called |
| 1250 |
useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }% |
\textbf{momViscosity, momAdvection, momForcing, useCoriolis, |
| 1251 |
\textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here. |
momPressureForcing, momStepping} and \textbf{metricTerms }and are |
| 1252 |
Look at the file \textit{model/inc/PARAMS.h }for a precise definition of |
assumed to be set to \texttt{'.TRUE.'} here. Look at the file |
| 1253 |
these variables. |
\textit{model/inc/PARAMS.h }for a precise definition of these |
| 1254 |
|
variables. |
| 1255 |
|
|
| 1256 |
\begin{description} |
\begin{description} |
| 1257 |
\item[initialization] \ |
\item[initialization] \ |
| 1263 |
\item[forcing] \ |
\item[forcing] \ |
| 1264 |
|
|
| 1265 |
This section only applies to the ocean. You need to generate |
This section only applies to the ocean. You need to generate |
| 1266 |
wind-stress data into two files \textbf{zonalWindFile}\textit{\ }and |
wind-stress data into two files \textbf{zonalWindFile} and |
| 1267 |
\textbf{ meridWindFile }corresponding to the zonal and meridional |
\textbf{meridWindFile} corresponding to the zonal and meridional |
| 1268 |
components of the wind stress, respectively (if you want the stress |
components of the wind stress, respectively (if you want the stress |
| 1269 |
to be along the direction of only one of the model horizontal axes, |
to be along the direction of only one of the model horizontal axes, |
| 1270 |
you only need to generate one file). The format of the files is |
you only need to generate one file). The format of the files is |
| 1271 |
similar to the bathymetry file. The zonal (meridional) stress data |
similar to the bathymetry file. The zonal (meridional) stress data |
| 1272 |
are assumed to be in Pa and located at U-points (V-points). As for |
are assumed to be in Pa and located at U-points (V-points). As for |
| 1273 |
the bathymetry, the precision with which to read the binary data is |
the bathymetry, the precision with which to read the binary data is |
| 1274 |
controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See |
controlled by the variable \textbf{readBinaryPrec}. See the matlab |
| 1275 |
the matlab program \textit{gendata.m }in the \textit{input |
program \textit{gendata.m} in the \textit{input} directories under |
| 1276 |
}directories under \textit{verification }to see how simple |
\textit{verification} to see how simple analytical wind forcing data |
| 1277 |
analytical wind forcing data are generated for the case study |
are generated for the case study experiments. |
|
experiments. |
|
| 1278 |
|
|
| 1279 |
There is also the possibility of prescribing time-dependent periodic |
There is also the possibility of prescribing time-dependent periodic |
| 1280 |
forcing. To do this, concatenate the successive time records into a |
forcing. To do this, concatenate the successive time records into a |
| 1281 |
single file (for each stress component) ordered in a (x, y, t) |
single file (for each stress component) ordered in a (x,y,t) fashion |
| 1282 |
fashion and set the following variables: |
and set the following variables: \textbf{periodicExternalForcing }to |
| 1283 |
\textbf{periodicExternalForcing }to '.\texttt{TRUE}.', |
\texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) |
| 1284 |
\textbf{externForcingPeriod }to the period (in s) of which the |
of which the forcing varies (typically 1 month), and |
| 1285 |
forcing varies (typically 1 month), and \textbf{externForcingCycle |
\textbf{externForcingCycle} to the repeat time (in s) of the forcing |
| 1286 |
}to the repeat time (in s) of the forcing (typically 1 year -- note: |
(typically 1 year -- note: \textbf{ externForcingCycle} must be a |
| 1287 |
\textbf{ externForcingCycle }must be a multiple of |
multiple of \textbf{externForcingPeriod}). With these variables set |
| 1288 |
\textbf{externForcingPeriod}). With these variables set up, the |
up, the model will interpolate the forcing linearly at each |
| 1289 |
model will interpolate the forcing linearly at each iteration. |
iteration. |
| 1290 |
|
|
| 1291 |
\item[dissipation] \ |
\item[dissipation] \ |
| 1292 |
|
|
| 1293 |
The lateral eddy viscosity coefficient is specified through the |
The lateral eddy viscosity coefficient is specified through the |
| 1294 |
variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The |
variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy |
| 1295 |
vertical eddy viscosity coefficient is specified through the |
viscosity coefficient is specified through the variable |
| 1296 |
variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and |
\textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and |
| 1297 |
\textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere. |
\textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere. The |
| 1298 |
The vertical diffusive fluxes can be computed implicitly by setting |
vertical diffusive fluxes can be computed implicitly by setting the |
| 1299 |
the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE} |
logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. |
| 1300 |
.'. In addition, biharmonic mixing can be added as well through the |
In addition, biharmonic mixing can be added as well through the |
| 1301 |
variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a |
variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar |
| 1302 |
spherical polar grid, you might also need to set the variable |
grid, you might also need to set the variable \textbf{cosPower} |
| 1303 |
\textbf{cosPower} which is set to 0 by default and which represents |
which is set to 0 by default and which represents the power of |
| 1304 |
the power of cosine of latitude to multiply viscosity. Slip or |
cosine of latitude to multiply viscosity. Slip or no-slip conditions |
| 1305 |
no-slip conditions at lateral and bottom boundaries are specified |
at lateral and bottom boundaries are specified through the logical |
| 1306 |
through the logical variables \textbf{no\_slip\_sides}\textit{\ } |
variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If |
| 1307 |
and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', |
set to \texttt{'.FALSE.'}, free-slip boundary conditions are |
| 1308 |
free-slip boundary conditions are applied. If no-slip boundary |
applied. If no-slip boundary conditions are applied at the bottom, a |
| 1309 |
conditions are applied at the bottom, a bottom drag can be applied |
bottom drag can be applied as well. Two forms are available: linear |
| 1310 |
as well. Two forms are available: linear (set the variable |
(set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and |
| 1311 |
\textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set |
quadratic (set the variable \textbf{bottomDragQuadratic} in |
| 1312 |
the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$). |
m$^{-1}$). |
| 1313 |
|
|
| 1314 |
The Fourier and Shapiro filters are described elsewhere. |
The Fourier and Shapiro filters are described elsewhere. |
| 1315 |
|
|
| 1323 |
\item[calculation of pressure/geopotential] \ |
\item[calculation of pressure/geopotential] \ |
| 1324 |
|
|
| 1325 |
First, to run a non-hydrostatic ocean simulation, set the logical |
First, to run a non-hydrostatic ocean simulation, set the logical |
| 1326 |
variable \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure |
variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure |
| 1327 |
field is then inverted through a 3D elliptic equation. (Note: this |
field is then inverted through a 3D elliptic equation. (Note: this |
| 1328 |
capability is not available for the atmosphere yet.) By default, a |
capability is not available for the atmosphere yet.) By default, a |
| 1329 |
hydrostatic simulation is assumed and a 2D elliptic equation is used |
hydrostatic simulation is assumed and a 2D elliptic equation is used |
| 1330 |
to invert the pressure field. The parameters controlling the |
to invert the pressure field. The parameters controlling the |
| 1331 |
behaviour of the elliptic solvers are the variables |
behaviour of the elliptic solvers are the variables |
| 1332 |
\textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual } for |
\textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for |
| 1333 |
the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{ |
the 2D case and \textbf{cg3dMaxIters} and |
| 1334 |
cg3dTargetResidual }for the 3D case. You probably won't need to |
\textbf{cg3dTargetResidual} for the 3D case. You probably won't need to |
| 1335 |
alter the default values (are we sure of this?). |
alter the default values (are we sure of this?). |
| 1336 |
|
|
| 1337 |
For the calculation of the surface pressure (for the ocean) or |
For the calculation of the surface pressure (for the ocean) or |
| 1338 |
surface geopotential (for the atmosphere) you need to set the |
surface geopotential (for the atmosphere) you need to set the |
| 1339 |
logical variables \textbf{rigidLid} and |
logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} |
| 1340 |
\textbf{implicitFreeSurface}\textit{\ }(set one to '. |
(set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} |
| 1341 |
\texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how |
depending on how you want to deal with the ocean upper or atmosphere |
| 1342 |
you want to deal with the ocean upper or atmosphere lower boundary). |
lower boundary). |
| 1343 |
|
|
| 1344 |
\end{description} |
\end{description} |
| 1345 |
|
|
| 1346 |
\subsection{Tracer equations} |
\subsection{Tracer equations} |
| 1347 |
|
|
| 1348 |
This section covers the tracer equations i.e. the potential temperature |
This section covers the tracer equations i.e. the potential |
| 1349 |
equation and the salinity (for the ocean) or specific humidity (for the |
temperature equation and the salinity (for the ocean) or specific |
| 1350 |
atmosphere) equation. As for the momentum equations, we only describe for |
humidity (for the atmosphere) equation. As for the momentum equations, |
| 1351 |
now the parameters that you are likely to change. The logical variables |
we only describe for now the parameters that you are likely to change. |
| 1352 |
\textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{ |
The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} |
| 1353 |
tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off |
\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn |
| 1354 |
terms in the temperature equation (same thing for salinity or specific |
on/off terms in the temperature equation (same thing for salinity or |
| 1355 |
humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{ |
specific humidity with variables \textbf{saltDiffusion}, |
| 1356 |
saltAdvection}\textit{\ }etc). These variables are all assumed here to be |
\textbf{saltAdvection} etc.). These variables are all assumed here to |
| 1357 |
set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a |
be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} |
| 1358 |
precise definition. |
for a precise definition. |
| 1359 |
|
|
| 1360 |
\begin{description} |
\begin{description} |
| 1361 |
\item[initialization] \ |
\item[initialization] \ |
| 1362 |
|
|
| 1363 |
The initial tracer data can be contained in the binary files |
The initial tracer data can be contained in the binary files |
| 1364 |
\textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files |
\textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files |
| 1365 |
should contain 3D data ordered in an (x, y, r) fashion with k=1 as |
should contain 3D data ordered in an (x,y,r) fashion with k=1 as the |
| 1366 |
the first vertical level. If no file names are provided, the |
first vertical level. If no file names are provided, the tracers |
| 1367 |
tracers are then initialized with the values of \textbf{tRef }and |
are then initialized with the values of \textbf{tRef} and |
| 1368 |
\textbf{sRef }mentioned above (in the equation of state section). In |
\textbf{sRef} mentioned above (in the equation of state section). In |
| 1369 |
this case, the initial tracer data are uniform in x and y for each |
this case, the initial tracer data are uniform in x and y for each |
| 1370 |
depth level. |
depth level. |
| 1371 |
|
|
| 1375 |
atmosphere not being completely stabilized at the moment. |
atmosphere not being completely stabilized at the moment. |
| 1376 |
|
|
| 1377 |
A combination of fluxes data and relaxation terms can be used for |
A combination of fluxes data and relaxation terms can be used for |
| 1378 |
driving the tracer equations. \ For potential temperature, heat flux |
driving the tracer equations. For potential temperature, heat flux |
| 1379 |
data (in W/m$ ^{2}$) can be stored in the 2D binary file |
data (in W/m$ ^{2}$) can be stored in the 2D binary file |
| 1380 |
\textbf{surfQfile}\textit{. } Alternatively or in addition, the |
\textbf{surfQfile}. Alternatively or in addition, the forcing can |
| 1381 |
forcing can be specified through a relaxation term. The SST data to |
be specified through a relaxation term. The SST data to which the |
| 1382 |
which the model surface temperatures are restored to are supposed to |
model surface temperatures are restored to are supposed to be stored |
| 1383 |
be stored in the 2D binary file \textbf{ thetaClimFile}\textit{. |
in the 2D binary file \textbf{thetaClimFile}. The corresponding |
| 1384 |
}The corresponding relaxation time scale coefficient is set through |
relaxation time scale coefficient is set through the variable |
| 1385 |
the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same |
\textbf{tauThetaClimRelax} (in s). The same procedure applies for |
| 1386 |
procedure applies for salinity with the variable names |
salinity with the variable names \textbf{EmPmRfile}, |
| 1387 |
\textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and |
\textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |
| 1388 |
\textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s) |
flux (in m/s) and surface salinity (in ppt) data files and |
| 1389 |
and surface salinity (in ppt) data files and relaxation time scale |
relaxation time scale coefficient (in s), respectively. Also for |
| 1390 |
coefficient (in s), respectively. Also for salinity, if the CPP key |
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |
| 1391 |
\textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions |
natural boundary conditions are applied i.e. when computing the |
| 1392 |
are applied i.e. when computing the surface salinity tendency, the |
surface salinity tendency, the freshwater flux is multiplied by the |
| 1393 |
freshwater flux is multiplied by the model surface salinity instead |
model surface salinity instead of a constant salinity value. |
|
of a constant salinity value. |
|
| 1394 |
|
|
| 1395 |
As for the other input files, the precision with which to read the |
As for the other input files, the precision with which to read the |
| 1396 |
data is controlled by the variable \textbf{readBinaryPrec}. |
data is controlled by the variable \textbf{readBinaryPrec}. |
| 1400 |
\item[dissipation] \ |
\item[dissipation] \ |
| 1401 |
|
|
| 1402 |
Lateral eddy diffusivities for temperature and salinity/specific |
Lateral eddy diffusivities for temperature and salinity/specific |
| 1403 |
humidity are specified through the variables \textbf{diffKhT }and |
humidity are specified through the variables \textbf{diffKhT} and |
| 1404 |
\textbf{diffKhS } (in m$^{2}$/s). Vertical eddy diffusivities are |
\textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are |
| 1405 |
specified through the variables \textbf{diffKzT }and \textbf{diffKzS |
specified through the variables \textbf{diffKzT} and |
| 1406 |
}(in m$^{2}$/s) for the ocean and \textbf{diffKpT }and |
\textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT |
| 1407 |
\textbf{diffKpS }(in Pa$^{2}$/s) for the atmosphere. The vertical |
}and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The |
| 1408 |
diffusive fluxes can be computed implicitly by setting the logical |
vertical diffusive fluxes can be computed implicitly by setting the |
| 1409 |
variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'. In |
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. |
| 1410 |
addition, biharmonic diffusivities can be specified as well through |
In addition, biharmonic diffusivities can be specified as well |
| 1411 |
the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in |
through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in |
| 1412 |
m$^{4}$/s). Note that the cosine power scaling (specified through |
m$^{4}$/s). Note that the cosine power scaling (specified through |
| 1413 |
\textbf{cosPower }- see the momentum equations section) is applied |
\textbf{cosPower}---see the momentum equations section) is applied to |
| 1414 |
to the tracer diffusivities (Laplacian and biharmonic) as well. The |
the tracer diffusivities (Laplacian and biharmonic) as well. The |
| 1415 |
Gent and McWilliams parameterization for oceanic tracers is |
Gent and McWilliams parameterization for oceanic tracers is |
| 1416 |
described in the package section. Finally, note that tracers can be |
described in the package section. Finally, note that tracers can be |
| 1417 |
also subject to Fourier and Shapiro filtering (see the corresponding |
also subject to Fourier and Shapiro filtering (see the corresponding |
| 1426 |
value (if set to a negative value by the user, the model will set it |
value (if set to a negative value by the user, the model will set it |
| 1427 |
to the tracer time step). The other option is to parameterize |
to the tracer time step). The other option is to parameterize |
| 1428 |
convection with implicit vertical diffusion. To do this, set the |
convection with implicit vertical diffusion. To do this, set the |
| 1429 |
logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .' |
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |
| 1430 |
and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) |
and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |
| 1431 |
you wish the tracer vertical diffusivities to have when mixing |
you wish the tracer vertical diffusivities to have when mixing |
| 1432 |
tracers vertically due to static instabilities. Note that |
tracers vertically due to static instabilities. Note that |
| 1433 |
\textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have |
\textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |
| 1434 |
non-zero value. |
value. |
| 1435 |
|
|
| 1436 |
\end{description} |
\end{description} |
| 1437 |
|
|
| 1438 |
\subsection{Simulation controls} |
\subsection{Simulation controls} |
| 1439 |
|
|
| 1440 |
The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s) |
The model ''clock'' is defined by the variable \textbf{deltaTClock} |
| 1441 |
which determines the IO frequencies and is used in tagging output. |
(in s) which determines the IO frequencies and is used in tagging |
| 1442 |
Typically, you will set it to the tracer time step for accelerated runs |
output. Typically, you will set it to the tracer time step for |
| 1443 |
(otherwise it is simply set to the default time step \textbf{deltaT}). |
accelerated runs (otherwise it is simply set to the default time step |
| 1444 |
Frequency of checkpointing and dumping of the model state are referenced to |
\textbf{deltaT}). Frequency of checkpointing and dumping of the model |
| 1445 |
this clock (see below). |
state are referenced to this clock (see below). |
| 1446 |
|
|
| 1447 |
\begin{description} |
\begin{description} |
| 1448 |
\item[run duration] \ |
\item[run duration] \ |
| 1449 |
|
|
| 1450 |
The beginning of a simulation is set by specifying a start time (in |
The beginning of a simulation is set by specifying a start time (in |
| 1451 |
s) through the real variable \textbf{startTime }or by specifying an |
s) through the real variable \textbf{startTime} or by specifying an |
| 1452 |
initial iteration number through the integer variable |
initial iteration number through the integer variable |
| 1453 |
\textbf{nIter0}. If these variables are set to nonzero values, the |
\textbf{nIter0}. If these variables are set to nonzero values, the |
| 1454 |
model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to |
model will look for a ''pickup'' file \textit{pickup.0000nIter0} to |
| 1455 |
restart the integration\textit{. }The end of a simulation is set |
restart the integration. The end of a simulation is set through the |
| 1456 |
through the real variable \textbf{endTime }(in s). Alternatively, |
real variable \textbf{endTime} (in s). Alternatively, you can |
| 1457 |
you can specify instead the number of time steps to execute through |
specify instead the number of time steps to execute through the |
| 1458 |
the integer variable \textbf{nTimeSteps}. |
integer variable \textbf{nTimeSteps}. |
| 1459 |
|
|
| 1460 |
\item[frequency of output] \ |
\item[frequency of output] \ |
| 1461 |
|
|
| 1462 |
Real variables defining frequencies (in s) with which output files |
Real variables defining frequencies (in s) with which output files |
| 1463 |
are written on disk need to be set up. \textbf{dumpFreq }controls |
are written on disk need to be set up. \textbf{dumpFreq} controls |
| 1464 |
the frequency with which the instantaneous state of the model is |
the frequency with which the instantaneous state of the model is |
| 1465 |
saved. \textbf{chkPtFreq } and \textbf{pchkPtFreq }control the |
saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output |
| 1466 |
output frequency of rolling and permanent checkpoint files, |
frequency of rolling and permanent checkpoint files, respectively. |
| 1467 |
respectively. See section 1.5.1 Output files for the definition of |
See section 1.5.1 Output files for the definition of model state and |
| 1468 |
model state and checkpoint files. In addition, time-averaged fields |
checkpoint files. In addition, time-averaged fields can be written |
| 1469 |
can be written out by setting the variable \textbf{taveFreq} (in s). |
out by setting the variable \textbf{taveFreq} (in s). The precision |
| 1470 |
The precision with which to write the binary data is controlled by |
with which to write the binary data is controlled by the integer |
| 1471 |
the integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} |
variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or |
| 1472 |
or \texttt{ 64}). |
\texttt{64}). |
| 1473 |
|
|
| 1474 |
\end{description} |
\end{description} |
| 1475 |
|
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