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In this section it is assumed that a programming environment has been properly setup. This environment may use either cmz or make to drive the preprocessing and compilation. You can skip the part related with the environment you don’t intend to use.
For instructions regarding the installation, see Installation.
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The user defined sequences are ‘KEEP’ in the cmz world. The most common organization is to have a cmz file in a subdirectory of the directory containing the mini_ker.cmz cmz file. In this cmz file there should be a ‘PATCH’ called ‘zinproc’ with the KEEPs within the patch. The KEEP must be called $zinit.
From within cmz in the directory of your model the source extraction,
compilation and linking will be triggered by a mod
command. This macro
uses the selseq.kumac information to find the mini_ker.cmz
cmz file.
mod
shall create a directory with the same name than the cmz file,
mymodel/ in our example. In this directory there is another
directory cfs/ containing the sources extracted from the cmz file.
The file mymodel_o.tmp contains all the mortran code generated
by cmz with the sequences substituted, including the $zinit. The fortran produced by the preprocessing and
splitting of this file is in files with the traditional ‘.f’ suffix.
The principal program is in principal.f. An efficient way of getting
familiar with mini_ker methods is looking at the mymodel_o.tmp where
all sequences and main Mortran instructions are gathered. Symbolic derivation
is noted as F_D(expression)(/variable)
, and the resulting Fortran code
is in principal.f.
mod
also triggers compilation and linking. The object files are in
the same cfs/ directory and the executable is in the mymodel/
directory, with name mymodel.exe.
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With make, the sequences are files ending with ‘.mti’ (for
mortran include files),
called, for example, zinit.mti.
They are included by
mortran
in other source files. You also need a Makefile
to drive the compilation of the model.
If you don’t need additional code or libraries to be linked with your model you have two alternatives.
start_miniker
script with the model file name as argument.
It should copy a zinit.mti file
ready to be edited and a Makefile ready to compile the model. For
the predator prey model, for example, you could run
$ start_miniker predator
model_file_name
variable to the name of your choice
in the Makefile. It is set to mymodel in the template. For the
predator-prey model, it could be set like
model_file_name = predator
If you want the executable model file to be built in another directory, you could set
model_file_name = some_dir/predator
The other items set in the default Makefile should be right.
The preprocessing and the compilation are launched with
make all
The mortran files are generated by the cmz directive preprocessor from files found in the package source directories. The mortran files end with ‘.mtn’ for the main files and ‘.mti’ for include files. They are output in the current directory. The mortran preprocessor then preprocess these mortran files and includes the sequences. The resulting fortran code is also in the current directory, in files with a ‘.f’ suffix. Some fortran files ending with ‘.F’ may also be created by the cmz directive preprocessor. The object files resulting from the compilation of all the fortran files (generated from mortran or directly from fortran files) are there too.
In case you want to override the default sequences or a subroutine file you just have to create it in your working directory along with the zinit.mti. For example you could want to create or modify a zsteer.mti file (see Executing code at the end of each time step), a zcmd_law.mti file (see Control laws), a monitor.f file (see Turning the model into a subroutine) to take advantage of features presented later in this manual.
More in-depth discussion of using make to run Miniker is covered in Advanced use of Miniker with make. For example it is also possible to create files that are to be preprocessed by the cmz directive preprocessor and separate source files and generated files. This advanced use is more precisely covered in Programming with cmz directives.
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Once compiled the model is ready to run, it only has to be executed. On standard output informations about the states, transfers, tangent linear system and other jacobian matrices are printed. For example the predator-prey model could be executed with:
./predator > result.lis
The correspondance between the symbolic variables and the basic vectors and functions are printed at run time:
---------------- Informing on Phi definition ----------------- Var-name, Function-name, index in ff vector ff_interact f_interact 1 ---------------------------------------------------- --------------- Informing on Eta definition ------------------ Var-name, Function-name, index in eta vector eta_prey deta_prey 1 eta_pred deta_pred 2
A summary of the model equations are in Model.hlp file. For the same example:
======================= set_Phi 1 ff_interact f_interact eta_pray*eta_pred ======================= set_Eta 1 eta_pray deta_pray apar*eta_pray-apar*ff_interact 2 eta_pred deta_pred -cpar*eta_pred+cpar*ff_interact
when other general functions are specified with f_set
, it can appear
also in the same help file when replaced by fun_set
.
As far as possible, all data printed in the listing are associated with a name related to a variable. Here is an extract:
Gamma :-8.19100E-02-1.42151E-01 3.87150E-02 eta_courant eta_T_czcx eta_T_sz ------------------------------------------------ Omega : 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 courant_L T_czcx Psi_Tczc Psi_Tsz ------------------------------------------------
for the two known vectors of the system, and:
>ker : Matrice de couplage 4 4 4 4 courant_L Raw(1,j=1,4): 1.000 -9.9010E-03 0.000 0.000 T_czcx Raw(2,j=1,4): -2.7972E-02 1.000 0.000 9.9900E-04 Psi_Tczcx Raw(3,j=1,4): 0.1605 9.7359E-02 1.000 -5.7321E-03 Psi_Tsz Raw(4,j=1,4): 0.000 -0.1376 5.7225E-03 1.000 Var-Name courant_L T_czcx Psi_Tczc Psi_Tsz ----------------------------------------------------------
where the couplage
(coupling matrix) is given that corresponds
to the matrix coupling the four transfer components after δη
has been eliminated from system. It is computed in the subprogram
oker (for kernel) which solves the system.
Basic results are output in a set of ‘.data’ files.
The first line (or two lines) describes the column with a ‘#’
character used to mark the lines as comments (for gnuplot
for example).
In the ‘.data’ files, the data are simply separated with spaces.
Each data file has the time
variable values as first column.
2.
Following columns give the values of eta(.)
in res.data,
dEta(.)
in dres.data – the step by step variation of
eta(.)
– and ff(.)
in tr.data.
Along the simulation the TEF Jacobian matrices are computed.
A transfer variables elimination process also leads to the definition
of the classical state advance matrix of the system
(the corresponding array is aspha(.,.)
in the code).
This matrix is output in the file aspha.data that is used to
post-run dynamics analyses. The matrix columns are written column wise on each
record.
See Stability analysis of fastest modes.
See Generalized
tangent linear system analysis. It is not used in the solving process.
Other ‘.data’ files will be described later.
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Since the data are simply separated with spaces, and comment lines
begin with ‘#’, the
files can be vizualised with many programs.
With gnuplot
, for example, to plot eta(n)
,
the gnuplot
statement could be:
plot "res.data" using 1:(n+1)
The similar one for ff(n)
:
plot "tr.data" using 1:(n+1)
For people using PAW
, the CERN graphical computer code,
Miniker prepares
kumacs that allow to read process the ‘.data’ files in the form of
n-tuples (see the PAW manual for more information).
In that cas, the flag sel paw
has to be gievn in the selsequ.kumac.
The generated n-tuples are ready to use only
for vector dimension of at most 10 (including the variable time
).
These kumacs are overwritten each time the model is run. Usaually, gnuplot has
to be preferred, but when using surfaces and histograms, PAW is better.
The gains.f (and go.xqt is provided as an example in the
Miniker files.
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This document was generated on a sunny day using texi2any.