/[MITgcm]/manual/s_examples/cfc_offline/offline_tutorial.tex
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# Line 7  Line 7 
7  % \begin{document}  % \begin{document}
8    
9  \section[Offline Example]{Offline Experiments}  \section[Offline Example]{Offline Experiments}
10  \label{www:tutorials}  %\label{www:tutorials}
11  \label{sect:eg-offline}  \label{sec:eg-offline}
12  \begin{center}  \begin{center}
13  (in directory: {\it verification/tutorial\_offline/}\\  (in directory: {\it verification/tutorial\_offline/})\\
14  \end{center}  \end{center}
15    
16  %\begin{center}  %\begin{center}
# Line 26  This document describes a simple experim Line 26  This document describes a simple experim
26  the MITgcm.  the MITgcm.
27    
28  \subsection{Overview}  \subsection{Overview}
29  \label{www:tutorials}  %\label{www:tutorials}
30    
31  This experiment demonstrates use of the offline form of the MITgcm to  This experiment demonstrates use of the offline form of the MITgcm to
32  study advection of a passive tracer. Time-averaged flow-fields and  study advection of a passive tracer. Time-averaged flow-fields and
33  mixing coefficients, deriving from a prior online run, are re-used  mixing coefficients, deriving from a prior online run, are re-used
34  leaving only the tracer equation to be integrated.  leaving only the tracer equation to be integrated.
35    
36  Figure \ref{FIG:eg-ofline_config} shows a movie of tracer being  Figure {\it --- missing figure ---} %\ref{fig:eg-ofline_config}
37    shows a movie of tracer being
38  advected using the offline package of the MITgcm. In the top panel the  advected using the offline package of the MITgcm. In the top panel the
39  frames of the movie show the monthly surface evolution of an initially  frames of the movie show the monthly surface evolution of an initially
40  local source of passive tracer. In the lower panel, the frames of the  local source of passive tracer. In the lower panel, the frames of the
# Line 41  movie show the changing monthly surface Line 42  movie show the changing monthly surface
42  tracer field had a global distribution.  tracer field had a global distribution.
43    
44  \subsection{Time-stepping of tracers}  \subsection{Time-stepping of tracers}
45  \label{www:tutorials}  %\label{www:tutorials}
46    
47  \noindent see section 2.15 through 2.18 for details of available  \noindent see section 2.15 through 2.18 for details of available
48  tracer time-stepping schemes and their characteristics.  tracer time-stepping schemes and their characteristics.
49    
50  \subsection{Code Configuration}  \subsection{Code Configuration}
51  \label{www:tutorials}  %\label{www:tutorials}
52  \label{SEC:eg_fourl_code_config}  \label{sec:eg_offl_code_config}
53    
54  \noindent The model configuration for this experiment resides under the  \noindent The model configuration for this experiment resides under the
55  directory {\it verification/tutorial\_offline}.  The experiment files  directory {\it verification/tutorial\_offline}.  The experiment files
# Line 79  files are required: Line 80  files are required:
80    
81    
82  \subsubsection{File {\it input/data}}  \subsubsection{File {\it input/data}}
83  \label{www:tutorials}  %\label{www:tutorials}
84    
85  \noindent This file, reproduced completely below, specifies the main  \noindent This file, reproduced completely below, specifies the main
86  parameters for the experiment.  parameters for the experiment.
# Line 189  $5200\,{\rm m}$. Line 190  $5200\,{\rm m}$.
190  \begin{itemize}  \begin{itemize}
191  \item Line 39  \item Line 39
192  \begin {verbatim}  \begin {verbatim}
193   phiMin=-90.,   ygOrigin=-90.,
194  \end{verbatim}  \end{verbatim}
195  \end{itemize}  \end{itemize}
196    
197  \noindent This line sets the southern boundary of the modeled domain  \noindent This line sets the southern boundary of the modeled domain
198  to $0^{\circ}$ latitude. This value affects both the generation of the  to $-90^{\circ}$ latitude N ($90^{\circ}$ S). This value affects both
199    the generation of the
200  locally orthogonal grid that the model uses internally and affects the  locally orthogonal grid that the model uses internally and affects the
201  initialization of the coriolis force.  Note - it is not required to  initialization of the coriolis force.  Note - it is not required to
202  set a longitude boundary, since the absolute longitude does not alter  set a longitude boundary, since the absolute longitude does not alter
# Line 278  this experiment, a depth of $0m$ indicat Line 280  this experiment, a depth of $0m$ indicat
280  36   delR=  50.,  70., 100., 140., 190.,  36   delR=  50.,  70., 100., 140., 190.,
281  37         240., 290., 340., 390., 440.,  37         240., 290., 340., 390., 440.,
282  38         490., 540., 590., 640., 690.,  38         490., 540., 590., 640., 690.,
283  39   phiMin=-90.,  39   ygOrigin=-90.,
284  40   dxSpacing=2.8125,  40   dxSpacing=2.8125,
285  41   dySpacing=2.8125,  41   dySpacing=2.8125,
286  42   &  42   &
# Line 290  this experiment, a depth of $0m$ indicat Line 292  this experiment, a depth of $0m$ indicat
292  \end{verbatim}  \end{verbatim}
293    
294  \subsubsection{File {\it input/data.off}}  \subsubsection{File {\it input/data.off}}
295  \label{www:tutorials}  %\label{www:tutorials}
296    
297  \noindent {\it input/data.off} provides the MITgcm offline package  \noindent {\it input/data.off} provides the MITgcm offline package
298  with package specific parameters. {\it input/data.off} specifies the  with package specific parameters. {\it input/data.off} specifies the
# Line 390  the value of the 10 digit sequencing tag Line 392  the value of the 10 digit sequencing tag
392    
393    
394  \subsubsection{File {\it input/data.pkg}}  \subsubsection{File {\it input/data.pkg}}
395  \label{www:tutorials}  %\label{www:tutorials}
396    
397  \noindent File {\it input/data.pkg}, reproduced completely below,  \noindent File {\it input/data.pkg}, reproduced completely below,
398  specifies which MITgcm packages ({\it ~/MITgcm/pkg}) are to be used.  specifies which MITgcm packages ({\it ~/MITgcm/pkg}) are to be used.
# Line 414  responsible for the advection of the tra Line 416  responsible for the advection of the tra
416  \end{verbatim}  \end{verbatim}
417    
418  \subsubsection{File {\it input/data.ptracers}}  \subsubsection{File {\it input/data.ptracers}}
419  \label{www:tutorials}  %\label{www:tutorials}
420    
421  \noindent File {\it input/data.ptracers}, reproduced completely below,  \noindent File {\it input/data.ptracers}, reproduced completely below,
422  provides the MITgcm ptracers package with package specific parameters,  provides the MITgcm ptracers package with package specific parameters,
# Line 516  manipulating initial tracer fields. Line 518  manipulating initial tracer fields.
518  each tracer.  each tracer.
519    
520  \subsubsection{File {\it input/eedata}}  \subsubsection{File {\it input/eedata}}
521  \label{www:tutorials}  %\label{www:tutorials}
522  \noindent This file uses standard default values and does not contain  \noindent This file uses standard default values and does not contain
523  customisations for this experiment.  customisations for this experiment.
524    
525  \noindent The following code changes are required to run this exaperiment.  \noindent The following code changes are required to run this exaperiment.
526    
527  \subsubsection{File {\it code/packages.conf}}  \subsubsection{File {\it code/packages.conf}}
528  \label{www:tutorials}  %\label{www:tutorials}
529    
530  \noindent This file is used to invoke the model components required  \noindent This file is used to invoke the model components required
531  for a particuylar implementation of the MITgcm. In this case the {\it  for a particuylar implementation of the MITgcm. In this case the {\it
# Line 542  offline Line 544  offline
544  \end{verbatim}  \end{verbatim}
545    
546  \subsubsection{File {\it code/PTRACERS\_SIZE.h}}  \subsubsection{File {\it code/PTRACERS\_SIZE.h}}
547  \label{www:tutorials}  %\label{www:tutorials}
548  \begin{itemize}  \begin{itemize}
549  \item Line  \item Line
550  \begin{verbatim}  \begin{verbatim}
# Line 555  tracers to be integrated) to 2 (in agree Line 557  tracers to be integrated) to 2 (in agree
557    input/data.ptracers}).    input/data.ptracers}).
558    
559  \subsubsection{File {\it code/SIZE.h}}  \subsubsection{File {\it code/SIZE.h}}
560  \label{www:tutorials}  %\label{www:tutorials}
561    
562  \noindent Two lines are customized in this file for the current  \noindent Two lines are customized in this file for the current
563  experiment  experiment
# Line 582  the vertical domain extent in grid point Line 584  the vertical domain extent in grid point
584    
585    
586  \subsection{Running The Example}  \subsection{Running The Example}
587  \label{www:tutorials}  %\label{www:tutorials}
588  \label{SEC:running_the_example}  %\label{sec:running_the_example}
589    
590  \subsubsection{Code Download}  \subsubsection{Code Download}
591  \label{www:tutorials}  %\label{www:tutorials}
592    
593  In order to run the examples you must first download the code  In order to run the examples you must first download the code
594  distribution.  Instructions for downloading the code can be found in  distribution.  Instructions for downloading the code can be found in
595  section \ref{sect:obtainingCode}.  section \ref{sec:obtainingCode}.
596    
597  \subsubsection{Experiment Location}  \subsubsection{Experiment Location}
598  \label{www:tutorials}  %\label{www:tutorials}
599    
600  This example experiment is located under the release sub-directory  This example experiment is located under the release sub-directory
601    
# Line 601  This example experiment is located under Line 603  This example experiment is located under
603  {\it verification/offline/ }  {\it verification/offline/ }
604    
605  \subsubsection{Running the Experiment}  \subsubsection{Running the Experiment}
606  \label{www:tutorials}  %\label{www:tutorials}
607    
608  To run the experiment  To run the experiment
609    
# Line 672  file pickup\_ptracers.0000000720.001.001 Line 674  file pickup\_ptracers.0000000720.001.001
674  nIter0 in file {\it run/data} to 720...  nIter0 in file {\it run/data} to 720...
675    
676  \subsection{A more complicated example}  \subsection{A more complicated example}
677  \label{sect:eg-offline-cfc}  \label{sec:eg-offline-cfc}
678  \begin{center}  \begin{center}
679  (in directory: {\it verification/tutorial\_cfc\_offline/}\\  (in directory: {\it verification/tutorial\_cfc\_offline/})\\
680  \end{center}  \end{center}
681    
682  \noindent The last example demonstrated simple advection of a passive  \noindent The last example demonstrated simple advection of a passive
# Line 739  GM_Kwy-T.0004248720.meta  Ttave.00042487 Line 741  GM_Kwy-T.0004248720.meta  Ttave.00042487
741    
742    
743  \subsubsection{File {\it input/data}}  \subsubsection{File {\it input/data}}
744  \label{www:tutorials}  %\label{www:tutorials}
745    
746  \noindent A single line must be added (under PARM01, between lines 6  \noindent A single line must be added (under PARM01, between lines 6
747  and 7) in file {\it input/data} from the previous example  and 7) in file {\it input/data} from the previous example
# Line 769  when it stops without error a dump will Line 771  when it stops without error a dump will
771    
772    
773  \subsubsection{File {\it input/data.off}}  \subsubsection{File {\it input/data.off}}
774  \label{www:tutorials}  %\label{www:tutorials}
775    
776  \noindent File {\it input/data.off}, reproduced in full below,  \noindent File {\it input/data.off}, reproduced in full below,
777  specifies the prefixes and locations of additional input files  specifies the prefixes and locations of additional input files
# Line 800  introduced with a non-zero starttime, at Line 802  introduced with a non-zero starttime, at
802  \end{verbatim}  \end{verbatim}
803    
804  \subsubsection{File {\it input/data.pkg}}  \subsubsection{File {\it input/data.pkg}}
805  \label{www:tutorials}  %\label{www:tutorials}
806    
807  \noindent File {\it input/data.pkg}, reproduced completely below,  \noindent File {\it input/data.pkg}, reproduced completely below,
808  specifies which MITgcm packages ({\it ~/MITgcm/pkg}) are to be used.  specifies which MITgcm packages ({\it ~/MITgcm/pkg}) are to be used.
# Line 818  It now invokes additional packages {\it Line 820  It now invokes additional packages {\it
820    
821    
822  \subsubsection{File {\it input/data.ptracers}}  \subsubsection{File {\it input/data.ptracers}}
823  \label{www:tutorials}  %\label{www:tutorials}
824    
825  \noindent File {\it input/data.ptracers}, reproduced completely below,  \noindent File {\it input/data.ptracers}, reproduced completely below,
826  specifies parameters associated with the CFC11 and CFC12 tracer fields  specifies parameters associated with the CFC11 and CFC12 tracer fields
# Line 893  pickup\_ptracers.0004269600.data Line 895  pickup\_ptracers.0004269600.data
895    
896    
897  \subsubsection{File {\it input/data.gchem}}  \subsubsection{File {\it input/data.gchem}}
898  \label{www:tutorials}  %\label{www:tutorials}
899    
900  \noindent File {\it input/data.gchem}, reproduced completely below,  \noindent File {\it input/data.gchem}, reproduced completely below,
901  names the forcing files needed in package GCHEM.  names the forcing files needed in package GCHEM.
# Line 928  surface wind fields. Line 930  surface wind fields.
930  \noindent Package GCHEM is described in detail in section ??  \noindent Package GCHEM is described in detail in section ??
931    
932  \subsubsection{File {\it input/data.gmredi}}  \subsubsection{File {\it input/data.gmredi}}
933  \label{www:tutorials}  %\label{www:tutorials}
934    
935  \noindent File {\it input/data.gmredi}, reproduced completely below,  \noindent File {\it input/data.gmredi}, reproduced completely below,
936  provides the parameters required for package GMREDI.  provides the parameters required for package GMREDI.
# Line 947  provides the parameters required for pac Line 949  provides the parameters required for pac
949  \noindent Package GMREDI is described in detail in section ??  \noindent Package GMREDI is described in detail in section ??
950    
951  \subsubsection{File {\it input/cfc1112.atm}}  \subsubsection{File {\it input/cfc1112.atm}}
952  \label{www:tutorials}  %\label{www:tutorials}
953    
954  \noindent File {\it input/cfc1112.atm} is a text file containing the  \noindent File {\it input/cfc1112.atm} is a text file containing the
955  CFC source functions over the northern and southern hemispheres  CFC source functions over the northern and southern hemispheres
956  annually from 1931 through 1998.  annually from 1931 through 1998.
957    
958  \subsubsection{File {\it code/packages.conf}}  \subsubsection{File {\it code/packages.conf}}
959  \label{www:tutorials}  %\label{www:tutorials}
960    
961  \noindent In this example {\it code/packages.conf} additionally  \noindent In this example {\it code/packages.conf} additionally
962  invokes components gchem, cfc and rmredi:  invokes components gchem, cfc and rmredi:
# Line 975  gmredi Line 977  gmredi
977  \end{verbatim}  \end{verbatim}
978    
979  \subsubsection{File {\it code/GCHEM\_OPTIONS.h}}  \subsubsection{File {\it code/GCHEM\_OPTIONS.h}}
980  \label{www:tutorials}  %\label{www:tutorials}
981    
982  \noindent File {\it code/GCHEM\_OPTIONS.h}, specifies options for  \noindent File {\it code/GCHEM\_OPTIONS.h}, specifies options for
983  package GCHEM. In this case defining the flag ALLOW\_CFC to activate  package GCHEM. In this case defining the flag ALLOW\_CFC to activate
984  the cfc code.  the cfc code.
985    
986  \subsubsection{File {\it code/GMREDI\_OPTIONS.h}}  \subsubsection{File {\it code/GMREDI\_OPTIONS.h}}
987  \label{www:tutorials}  %\label{www:tutorials}
988    
989  \noindent File {\it code/GCHEM\_OPTIONS.h}, specifies options for  \noindent File {\it code/GCHEM\_OPTIONS.h}, specifies options for
990  package GMREDI.  package GMREDI.
991    
992  \subsubsection{File {\it code/PTRACERS\_SIZE.h}}  \subsubsection{File {\it code/PTRACERS\_SIZE.h}}
993  \label{www:tutorials}  %\label{www:tutorials}
994    
995  \noindent File {\it code/PTRACERS\_SIZE.h} is unchanged from the  \noindent File {\it code/PTRACERS\_SIZE.h} is unchanged from the
996  simpler example.  simpler example.
997    
998  \subsubsection{File {\it code/SIZE.h}}  \subsubsection{File {\it code/SIZE.h}}
999  \label{www:tutorials}  %\label{www:tutorials}
1000    
1001  \noindent File {\it code/SIZE.h} is unchanged from the simpler  \noindent File {\it code/SIZE.h} is unchanged from the simpler
1002  example.  example.
1003    
1004    
1005  \subsubsection{Running the Experiment}  \subsubsection{Running the Experiment}
1006  \label{www:tutorials}  %\label{www:tutorials}
1007    
1008  The model is run as before and produces the files the model generates  The model is run as before and produces the files the model generates
1009  describing the grid (prefixed Depth, DXC, DXG, hFacC, hFacS and hFacW)  describing the grid (prefixed Depth, DXC, DXG, hFacC, hFacS and hFacW)
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