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revision 1.1.1.1 by adcroft, Wed Aug 8 16:15:31 2001 UTC revision 1.7 by cnh, Sun Oct 21 04:19:40 2001 UTC
# Line 1  Line 1 
1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4    %\section{Getting started}
5    
6  \begin{center}  In this section, we describe how to use the model. In the first
7  {\Large \textbf{Using the model}}  section, we provide enough information to help you get started with
8    the model. We believe the best way to familiarize yourself with the
9    model is to run the case study examples provided with the base
10    version. Information on how to obtain, compile, and run the code is
11    found there as well as a brief description of the model structure
12    directory and the case study examples.  The latter and the code
13    structure are described more fully in chapters
14    \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
15    this section, we provide information on how to customize the code when
16    you are ready to try implementing the configuration you have in mind.
17    
18    \section{Where to find information}
19    \label{sect:whereToFindInfo}
20    
21    A web site is maintained for release 1 (Sealion) of MITgcm:
22    \begin{verbatim}
23    http://mitgcm.org/sealion
24    \end{verbatim}
25    Here you will find an on-line version of this document, a
26    ``browsable'' copy of the code and a searchable database of the model
27    and site, as well as links for downloading the model and
28    documentation, to data-sources and other related sites.
29    
30  \vspace*{4mm}  There is also a support news group for the model that you can email at
31    \texttt{support@mitgcm.org} or browse at:
 \vspace*{3mm} {\large July 2001}  
 \end{center}  
   
 In this part, we describe how to use the model. In the first section, we  
 provide enough information to help you get started with the model. We  
 believe the best way to familiarize yourself with the model is to run the  
 case study examples provided with the base version. Information on how to  
 obtain, compile, and run the code is found there as well as a brief  
 description of the model structure directory and the case study examples.  
 The latter and the code structure are described more fully in sections 2 and  
 3, respectively. In section 4, we provide information on how to customize  
 the code when you are ready to try implementing the configuration you have  
 in mind.  
   
 \section{Getting started}  
   
 \subsection{Obtaining the code}  
   
 The reference web site for the model is:  
 \begin{verbatim}  
 http://mitgcm.org  
 \end{verbatim}  
   
 On this site, you can download the model as well as find useful information,  
 some of which might overlap with what is written here. There is also a  
 support news group for the model located at (send your message to \texttt{%  
 support@mitgcm.org}):  
32  \begin{verbatim}  \begin{verbatim}
33  news://mitgcm.org/mitgcm.support  news://mitgcm.org/mitgcm.support
34  \end{verbatim}  \end{verbatim}
35    A mail to the email list will reach all the developers and be archived
36    on the newsgroup. A users email list will be established at some time
37    in the future.
38    
39    \section{Obtaining the code}
40    \label{sect:obtainingCode}
41    
42    MITgcm can be downloaded from our system by following
43    the instructions below. As a courtesy we ask that you send e-mail to us at
44    \begin{rawhtml} <A href=mailto:support@mitgcm.org> \end{rawhtml}
45    support@mitgcm.org
46    \begin{rawhtml} </A> \end{rawhtml}
47    to enable us to keep track of who's using the model and in what application.
48    You can download the model two ways:
49    
50    \begin{enumerate}
51    \item Using CVS software. CVS is a freely available source code managment
52    tool. To use CVS you need to have the software installed. Many systems
53    come with CVS pre-installed, otherwise good places to look for
54    the software for a particular platform are
55    \begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
56    cvshome.org
57    \begin{rawhtml} </A> \end{rawhtml}
58    and
59    \begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
60    wincvs.org
61    \begin{rawhtml} </A> \end{rawhtml}
62    .
63    
64    \item Using a tar file. This method is simple and does not
65    require any special software. However, this method does not
66    provide easy support for maintenance updates.
67    
68    \end{enumerate}
69    
70  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
71  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
72  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
73  download a tar file.  download a tar file.
74    
 \subsubsection{using CVS}  
   
75  Before you can use CVS, the following environment variable has to be set in  Before you can use CVS, the following environment variable has to be set in
76  your .cshrc or .tcshrc:  your .cshrc or .tcshrc:
77  \begin{verbatim}  \begin{verbatim}
78  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
79    \end{verbatim}
80    
81    To start using CVS, register with the MITgcm CVS server using command:
82    \begin{verbatim}
83  % cvs login ( CVS password: cvsanon )  % cvs login ( CVS password: cvsanon )
84  \end{verbatim}  \end{verbatim}
85    You only need to do ``cvs login'' once.
86    
87  You only need to do ``cvs login'' once. To obtain the latest source:  To obtain the sources for release1 type:
88  \begin{verbatim}  \begin{verbatim}
89  % cvs co -d directory models/MITgcmUV  % cvs co -d directory -P -r release1 MITgcmUV
90  \end{verbatim}  \end{verbatim}
91    
92  This creates a directory called \textit{directory}. If \textit{directory}  This creates a directory called \textit{directory}. If \textit{directory}
93  exists this command updates your code based on the repository. Each  exists this command updates your code based on the repository. Each
94  directory in the source tree contains a directory \textit{CVS}. This  directory in the source tree contains a directory \textit{CVS}. This
95  information is required by CVS to keep track of your file versions with  information is required by CVS to keep track of your file versions with
96  respect to the repository. Don't edit the files in \textit{CVS}! To obtain a  respect to the repository. Don't edit the files in \textit{CVS}!
97  specific \textit{version} that is not the latest source:  You can also use CVS to download code updates.  More extensive
98  \begin{verbatim}  information on using CVS for maintaining MITgcm code can be found
99  % cvs co -d directory -r version models/MITgcmUV  \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
100  \end{verbatim}  here
101    \begin{rawhtml} </A> \end{rawhtml}
102    .
103    
 \subsubsection{other methods}  
104    
105  You can download the model as a tar file from the reference web site at:  \paragraph*{Conventional download method}
106    \label{sect:conventionalDownload}
107    
108    If you do not have CVS on your system, you can download the model as a
109    tar file from the reference web site at:
110    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
111  \begin{verbatim}  \begin{verbatim}
112  http://mitgcm.org/download/  http://mitgcm.org/download/
113  \end{verbatim}  \end{verbatim}
114    \begin{rawhtml} </A> \end{rawhtml}
115    The tar file still contains CVS information which we urge you not to
116    delete; even if you do not use CVS yourself the information can help
117    us if you should need to send us your copy of the code.
118    
119  \subsection{Model and directory structure}  \section{Model and directory structure}
120    
121  The ``numerical'' model is contained within a execution environment support  The ``numerical'' model is contained within a execution environment support
122  wrapper. This wrapper is designed to provide a general framework for  wrapper. This wrapper is designed to provide a general framework for
# Line 124  the makefile specific to the Tangent lin Line 166  the makefile specific to the Tangent lin
166  generates the adjoint code. The latter is described in details in part V.  generates the adjoint code. The latter is described in details in part V.
167    
168  \item \textit{utils}: this directory contains various utilities. The  \item \textit{utils}: this directory contains various utilities. The
169  subdirectory \textit{knudsen2} contains code and a makefile that compute  subdirectory \textit{knudsen2} contains code and a makefile that
170  coefficients of the polynomial approximation to the knudsen formula for an  compute coefficients of the polynomial approximation to the knudsen
171  ocean nonlinear equation of state. The \textit{matlab} subdirectory contains  formula for an ocean nonlinear equation of state. The \textit{matlab}
172  matlab scripts for reading model output directly into matlab. \textit{scripts%  subdirectory contains matlab scripts for reading model output directly
173  } contains C-shell post-processing scripts for joining processor-based and  into matlab. \textit{scripts} contains C-shell post-processing
174  tiled-based model output.  scripts for joining processor-based and tiled-based model output.
175    
176  \item \textit{verification}: this directory contains the model examples. See  \item \textit{verification}: this directory contains the model examples. See
177  below.  section \ref{sect:modelExamples}.
178  \end{itemize}  \end{itemize}
179    
180  \subsection{Model examples}  \section{Example experiments}
181    \label{sect:modelExamples}
182    
183  Now that you have successfully downloaded the model code we recommend that  Now that you have successfully downloaded the model code we recommend that
184  you first try to run the examples provided with the base version. You will  you first try to run the examples provided with the base version. You will
# Line 144  you will use eventually. The examples ar Line 187  you will use eventually. The examples ar
187  the directory \textit{verification} and are briefly described below (a full  the directory \textit{verification} and are briefly described below (a full
188  description is given in section 2):  description is given in section 2):
189    
190  \subsubsection{List of model examples}  \subsection{List of model examples}
191    
192  \begin{itemize}  \begin{itemize}
193  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
# Line 198  Molteni physics package. Global configur Line 241  Molteni physics package. Global configur
241  \item \textit{adjustment.cs-32x32x1}  \item \textit{adjustment.cs-32x32x1}
242  \end{itemize}  \end{itemize}
243    
244  \subsubsection{Directory structure of model examples}  \subsection{Directory structure of model examples}
245    
246  Each example directory has the following subdirectories:  Each example directory has the following subdirectories:
247    
# Line 250  comparison with your own output when you Line 293  comparison with your own output when you
293  Once you have chosen the example you want to run, you are ready to compile  Once you have chosen the example you want to run, you are ready to compile
294  the code.  the code.
295    
296  \subsection{Compiling the code}  \section{Building the code}
297    \label{sect:buildingCode}
298    
299    To compile the code, we use the {\em make} program. This uses a file
300    ({\em Makefile}) that allows us to pre-process source files, specify
301    compiler and optimization options and also figures out any file
302    dependancies. We supply a script ({\em genmake}), described in section
303    \ref{sect:genmake}, that automatically creates the {\em Makefile} for
304    you. You then need to build the dependancies and compile the code.
305    
306    As an example, let's assume that you want to build and run experiment
307    \textit{verification/exp2}. The are multiple ways and places to actually
308    do this but here let's build the code in
309    \textit{verification/exp2/input}:
310    \begin{verbatim}
311    % cd verification/exp2/input
312    \end{verbatim}
313    First, build the {\em Makefile}:
314    \begin{verbatim}
315    % ../../../tools/genmake -mods=../code
316    \end{verbatim}
317    The command line option tells {\em genmake} to override model source
318    code with any files in the directory {\em ./code/}.
319    
320    If there is no \textit{.genmakerc} in the \textit{input} directory, you have
321    to use the following options when invoking \textit{genmake}:
322    \begin{verbatim}
323    % ../../../tools/genmake  -mods=../code
324    \end{verbatim}
325    
326    Next, create the dependancies:
327    \begin{verbatim}
328    % make depend
329    \end{verbatim}
330    This modifies {\em Makefile} by attaching a [long] list of files on
331    which other files depend. The purpose of this is to reduce
332    re-compilation if and when you start to modify the code. {\tt make
333    depend} also created links from the model source to this directory.
334    
335    Now compile the code:
336    \begin{verbatim}
337    % make
338    \end{verbatim}
339    The {\tt make} command creates an executable called \textit{mitgcmuv}.
340    
341    Now you are ready to run the model. General instructions for doing so are
342    given in section \ref{sect:runModel}. Here, we can run the model with:
343    \begin{verbatim}
344    ./mitgcmuv > output.txt
345    \end{verbatim}
346    where we are re-directing the stream of text output to the file {\em
347    output.txt}.
348    
349    
350    \subsection{Building/compiling the code elsewhere}
351    
352    In the example above (section \ref{sect:buildingCode}) we built the
353    executable in the {\em input} directory of the experiment for
354    convenience. You can also configure and compile the code in other
355    locations, for example on a scratch disk with out having to copy the
356    entire source tree. The only requirement to do so is you have {\tt
357    genmake} in your path or you know the absolute path to {\tt genmake}.
358    
359    The following sections outline some possible methods of organizing you
360    source and data.
361    
362    \subsubsection{Building from the {\em ../code directory}}
363    
364    This is just as simple as building in the {\em input/} directory:
365    \begin{verbatim}
366    % cd verification/exp2/code
367    % ../../../tools/genmake
368    % make depend
369    % make
370    \end{verbatim}
371    However, to run the model the executable ({\em mitgcmuv}) and input
372    files must be in the same place. If you only have one calculation to make:
373    \begin{verbatim}
374    % cd ../input
375    % cp ../code/mitgcmuv ./
376    % ./mitgcmuv > output.txt
377    \end{verbatim}
378    or if you will be making muliple runs with the same executable:
379    \begin{verbatim}
380    % cd ../
381    % cp -r input run1
382    % cp code/mitgcmuv run1
383    % cd run1
384    % ./mitgcmuv > output.txt
385    \end{verbatim}
386    
387    \subsubsection{Building from a new directory}
388    
389    Since the {\em input} directory contains input files it is often more
390    useful to keep {\em input} prestine and build in a new directory
391    within {\em verification/exp2/}:
392    \begin{verbatim}
393    % cd verification/exp2
394    % mkdir build
395    % cd build
396    % ../../../tools/genmake -mods=../code
397    % make depend
398    % make
399    \end{verbatim}
400    This builds the code exactly as before but this time you need to copy
401    either the executable or the input files or both in order to run the
402    model. For example,
403    \begin{verbatim}
404    % cp ../input/* ./
405    % ./mitgcmuv > output.txt
406    \end{verbatim}
407    or if you tend to make multiple runs with the same executable then
408    running in a new directory each time might be more appropriate:
409    \begin{verbatim}
410    % cd ../
411    % mkdir run1
412    % cp build/mitgcmuv run1/
413    % cp input/* run1/
414    % cd run1
415    % ./mitgcmuv > output.txt
416    \end{verbatim}
417    
418    \subsubsection{Building from on a scratch disk}
419    
420    Model object files and output data can use up large amounts of disk
421    space so it is often the case that you will be operating on a large
422    scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
423    following commands will build the model in {\em /scratch/exp2-run1}:
424    \begin{verbatim}
425    % cd /scratch/exp2-run1
426    % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
427    % make depend
428    % make
429    \end{verbatim}
430    To run the model here, you'll need the input files:
431    \begin{verbatim}
432    % cp ~/MITgcm/verification/exp2/input/* ./
433    % ./mitgcmuv > output.txt
434    \end{verbatim}
435    
436    As before, you could build in one directory and make multiple runs of
437    the one experiment:
438    \begin{verbatim}
439    % cd /scratch/exp2
440    % mkdir build
441    % cd build
442    % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
443    % make depend
444    % make
445    % cd ../
446    % cp -r ~/MITgcm/verification/exp2/input run2
447    % cd run2
448    % ./mitgcmuv > output.txt
449    \end{verbatim}
450    
451  \subsubsection{The script \textit{genmake}}  
452    
453    \subsection{\textit{genmake}}
454    \label{sect:genmake}
455    
456  To compile the code, use the script \textit{genmake} located in the \textit{%  To compile the code, use the script \textit{genmake} located in the \textit{%
457  tools} directory. \textit{genmake} is a script that generates the makefile.  tools} directory. \textit{genmake} is a script that generates the makefile.
# Line 353  For some of the examples, there is a fil Line 552  For some of the examples, there is a fil
552  that particular example. In this way you don't need to type the options when  that particular example. In this way you don't need to type the options when
553  invoking \textit{genmake}.  invoking \textit{genmake}.
554    
 \subsubsection{Compiling}  
555    
556  Let's assume that you want to run, say, example \textit{exp2} in the \textit{%  \section{Running the model}
557  input} directory. To compile the code, type the following commands from the  \label{sect:runModel}
 model root tree:  
 \begin{verbatim}  
 % cd verification/exp2/input  
 % ../../../tools/genmake  
 % make depend  
 % make  
 \end{verbatim}  
558    
559  If there is no \textit{.genmakerc} in the \textit{input} directory, you have  If compilation finished succesfuully (section \ref{sect:buildModel})
560  to use the following options when invoking \textit{genmake}:  then an executable called {\em mitgcmuv} will now exist in the local
561  \begin{verbatim}  directory.
 % ../../../tools/genmake  -mods=../code  
 \end{verbatim}  
562    
563  In addition, you will probably want to disable some of the packages. Taking  To run the model as a single process (ie. not in parallel) simply
564  again the case of \textit{exp2}, the full \textit{genmake} command will  type:
 probably look like this:  
565  \begin{verbatim}  \begin{verbatim}
566  % ../../../tools/genmake  -mods=../code  -disable=kpp,gmredi,aim,...  % ./mitgcmuv
567  \end{verbatim}  \end{verbatim}
568    The ``./'' is a safe-guard to make sure you use the local executable
569  The make command creates an executable called \textit{mitgcmuv}.  in case you have others that exist in your path (surely odd if you
570    do!). The above command will spew out many lines of text output to
571  Note that you can compile and run the code in another directory than \textit{%  your screen.  This output contains details such as parameter values as
572  input}. You just need to make sure that you copy the input data files into  well as diagnostics such as mean Kinetic energy, largest CFL number,
573  the directory where you want to run the model. For example to compile from  etc. It is worth keeping this text output with the binary output so we
574  \textit{code}:  normally re-direct the {\em stdout} stream as follows:
575  \begin{verbatim}  \begin{verbatim}
576  % cd verification/exp2/code  % ./mitgcmuv > output.txt
 % ../../../tools/genmake  
 % make depend  
 % make  
577  \end{verbatim}  \end{verbatim}
578    
579  \subsection{Running the model}  For the example experiments in {\em vericication}, an example of the
580    output is kept in {\em results/output.txt} for comparison. You can compare
581    your {\em output.txt} with this one to check that the set-up works.
582    
 The first thing to do is to run the code by typing \textit{mitgcmuv} and see  
 what happens. You can compare what you get with what is in the \textit{%  
 results} directory. Unless noted otherwise, most examples are set up to run  
 for a few time steps only so that you can quickly figure out whether the  
 model is working or not.  
583    
584  \subsubsection{Output files}  
585    \subsection{Output files}
586    
587  The model produces various output files. At a minimum, the instantaneous  The model produces various output files. At a minimum, the instantaneous
588  ``state'' of the model is written out, which is made of the following files:  ``state'' of the model is written out, which is made of the following files:
# Line 450  as the pickup files but are named differ Line 633  as the pickup files but are named differ
633  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
634  output to save disk space during long integrations.  output to save disk space during long integrations.
635    
636  \subsubsection{Looking at the output}  \subsection{Looking at the output}
637    
638  All the model data are written according to a ``meta/data'' file format.  All the model data are written according to a ``meta/data'' file format.
639  Each variable is associated with two files with suffix names \textit{.data}  Each variable is associated with two files with suffix names \textit{.data}
# Line 464  written in this format. The matlab scrip Line 647  written in this format. The matlab scrip
647  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads
648  the data. Look at the comments inside the script to see how to use it.  the data. Look at the comments inside the script to see how to use it.
649    
650  \section{Code structure}  Some examples of reading and visualizing some output in {\em Matlab}:
651    \begin{verbatim}
652    % matlab
653    >> H=rdmds('Depth');
654    >> contourf(H');colorbar;
655    >> title('Depth of fluid as used by model');
656    
657    >> eta=rdmds('Eta',10);
658    >> imagesc(eta');axis ij;colorbar;
659    >> title('Surface height at iter=10');
660    
661  \section{Doing it yourself: customizing the code}  >> eta=rdmds('Eta',[0:10:100]);
662    >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
663    \end{verbatim}
664    
665  \subsection{\protect\bigskip Configuration and setup}  \section{Doing it yourself: customizing the code}
666    
667  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
668  easiest thing is to use and adapt the setup of the case studies experiment  easiest thing is to use and adapt the setup of the case studies experiment
# Line 478  relative to the ''numerical model'' part Line 672  relative to the ''numerical model'' part
672  the ''execution environment'' part is covered in the parallel implementation  the ''execution environment'' part is covered in the parallel implementation
673  section) and on the variables and parameters that you are likely to change.  section) and on the variables and parameters that you are likely to change.
674    
675    \subsection{Configuration and setup}
676    
677  The CPP keys relative to the ''numerical model'' part of the code are all  The CPP keys relative to the ''numerical model'' part of the code are all
678  defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%  defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
679  model/inc }or in one of the \textit{code }directories of the case study  model/inc }or in one of the \textit{code }directories of the case study
# Line 494  In what follows the parameters are group Line 690  In what follows the parameters are group
690  computational domain, the equations solved in the model, and the simulation  computational domain, the equations solved in the model, and the simulation
691  controls.  controls.
692    
693  \subsubsection{Computational domain, geometry and time-discretization}  \subsection{Computational domain, geometry and time-discretization}
694    
695  \begin{itemize}  \begin{itemize}
696  \item dimensions  \item dimensions
# Line 586  parameter is set through the variable \t Line 782  parameter is set through the variable \t
782  stagger baroclinic time stepping can be activated by setting the logical  stagger baroclinic time stepping can be activated by setting the logical
783  variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.  variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.
784    
785  \subsubsection{Equation of state}  \subsection{Equation of state}
786    
787  First, because the model equations are written in terms of perturbations, a  First, because the model equations are written in terms of perturbations, a
788  reference thermodynamic state needs to be specified. This is done through  reference thermodynamic state needs to be specified. This is done through
# Line 615  available in the same directory and you Line 811  available in the same directory and you
811  values of the vertical levels in \textit{knudsen2.f }so that they match  values of the vertical levels in \textit{knudsen2.f }so that they match
812  those of your configuration). \textit{\ }  those of your configuration). \textit{\ }
813    
814  \subsubsection{Momentum equations}  \subsection{Momentum equations}
815    
816  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 likely
817  to change, i.e. the ones relative to forcing and dissipation for example.  to change, i.e. the ones relative to forcing and dissipation for example.
# Line 719  geopotential (for the atmosphere) you ne Line 915  geopotential (for the atmosphere) you ne
915  \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you  \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
916  want to deal with the ocean upper or atmosphere lower boundary).  want to deal with the ocean upper or atmosphere lower boundary).
917    
918  \subsubsection{Tracer equations}  \subsection{Tracer equations}
919    
920  This section covers the tracer equations i.e. the potential temperature  This section covers the tracer equations i.e. the potential temperature
921  equation and the salinity (for the ocean) or specific humidity (for the  equation and the salinity (for the ocean) or specific humidity (for the
# Line 810  wish the tracer vertical diffusivities t Line 1006  wish the tracer vertical diffusivities t
1006  vertically due to static instabilities. Note that \textbf{cadjFreq }and  vertically due to static instabilities. Note that \textbf{cadjFreq }and
1007  \textbf{ivdc\_kappa }can not both have non-zero value.  \textbf{ivdc\_kappa }can not both have non-zero value.
1008    
1009  \subsubsection{Simulation controls}  \subsection{Simulation controls}
1010    
1011  The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)  The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)
1012  which determines the IO frequencies and is used in tagging output.  which determines the IO frequencies and is used in tagging output.
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