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Hiroaki Matsui authored and Hiroaki Matsui committed Aug 10, 2023
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51 changes: 38 additions & 13 deletions doc/tex_src/controls_CALYPSO.tex
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ \subsection{Block {\tt data\_files\_def}}
\paragraph{\tt sph\_file\_fmt\_ctl}
\label{href_t:sph_file_fmt_ctl}
\verb|[sph_formayt]| \\
File format of spherical harmonics indexing and FEM mesh file \verb|[sph_format]| is defined by text. Following data formats can be defined. Extensions of each data format is listed in Table \ref{table:mesh_format}.
File format of spherical harmonics indexing and FEM mesh file \verb|[sph_format]| is defined by text. Following data formats can be defined. Flags of each data format is listed in Table \ref{table:mesh_format}.
%
\begin{description}
\item{\tt ascii: } Distributed ASCII data
Expand All @@ -73,7 +73,7 @@ \subsection{Block {\tt data\_files\_def}}
\paragraph{\tt restart\_file\_fmt\_ctl}
\label{href_t:restart_file_fmt_ctl}
\verb|[rst_format]| \\
File format of restart files \verb|[rst_format]| is defined by text. Following data formats can be defined. Extensions of each data format is listed in Table \ref{table:restart_format}.
File format of restart files \verb|[rst_format]| is defined by text. Following data formats can be defined. Flags of each data format is listed in Table \ref{table:restart_format}.
%
\begin{description}
\item{\tt ascii: } Distributed ASCII data
Expand Down Expand Up @@ -144,7 +144,7 @@ \subsubsection{\tt num\_domain\_ctl}
\paragraph{\tt num\_horizontal\_domain\_ctl}
\label{href_t:num_horizontal_domain_ctl}
\verb|[Ndomain]| \\
Number of subdomains in the horizontal direction. The number will be the number of subdomains for the meridional directios for the spherical grid $(r, \theta, \phi)$ and Fourier transform $(r, \theta, m)$. For Legendre transform $(r, \theta, m)$ and $(r, l, m)$, the number will be the number of subdomains for the h.armonics ordedr $m$.
Number of subdomains in the horizontal direction. The number will be the number of subdomains for the meridional directios for the spherical grid $(r, \theta, \phi)$ and Fourier transform $(r, \theta, m)$. For Legendre transform $(r, \theta, m)$ and $(r, l, m)$, the number will be the number of subdomains for the harmonics ordedr $m$.


\paragraph{\color{magenta} \tt num\_domain\_sph\_grid [Direction] [Ndomain]}
Expand All @@ -163,34 +163,54 @@ \subsubsection{\tt num\_domain\_ctl}
Definition of number of subdomains for spectrum data in $(r, l, m)$. Direction {\tt modes} is set in the \verb|[Direction]| field, and number of subdomains \verb|[Ndomain]| are defined in the integer field.


\subsubsection{\tt num\_grid\_sph}
\subsubsection{{\tt shell\_define\_ctl} (Previously {\tt num\_grid\_sph})}
\label{href_t:num_grid_sph}
Spatial resolution of the spherical shell is defined in this block. \\
Spatial resolution of the spherical shell is defined in this block. Old block name \verb|num_grid_sph| is also accept as this block label.\\
\hyperref[href_i:num_grid_sph]{(Back to {\tt control\_sph\_shell})}

\paragraph{\tt sph\_center\_coef\_ctl}
\label{href_t:sph_center_coef_ctl}
\verb|[TYPE]| \\
Set flag \verb|with_center| into \verb|[type]| to include spherical harmonics coefficient for $l = m = 0$. This fliag is required when temperature or composition is solved to the center.

\paragraph{\tt sph\_grid\_type\_ctl}
\label{href_t:sph_grid_type_ctl}
\verb|[TYPE]| \\
Set spherical shell grid type for visualization. The follwing types are avaiable. Default value is \verb|no_pole|. The following flags are avaiable.
%
\begin{description}
\item{\tt no\_pole} Spherical shell grid is only generated from grids on Gauss-Legendle points on latitude. Corequently, small empty tube (circle on a sphere surface) has to be made in visualization.
\item{\tt with\_pole} Grid points are added at poles in the grids. There is still empty sphere in the whole sphre grid.
\item{\tt with\_center} Grid at poles and centere is added in the grid. The mesh inceludes center is degenerated from hexahedral mesh to pyramid mesh. This mode increases initialization time.
\end{description}
%

\paragraph{\tt truncation\_level\_ctl}
\label{href_t:truncation_level_ctl}
\verb|[Lmax]| \\
Truncation level $L$ is defined by integer. Spherical harmonics is truncated by triangular $0 \le l \le L$ and $0 <m < l$.

\paragraph{\tt longitude\_symmetry\_ctl [M\_sym]}
\label{href_t:longitude_symmetry_ctl}
Longitudinal folding symmtery \verb|[M_sym]| is defeined by integer.

\paragraph{\tt ngrid\_meridonal\_ctl}
\label{href_t:ngrid_meridonal_ctl}
\verb|[Ntheta]| \\
Number of grid in the meridional direction \verb|[Ntheta]| is defined by integer
\paragraph{\tt ngrid\_zonal\_ctl}
Number of grid in the meridional direction $N_{\theta}$ is defined by integer \verb|[Ntheta]|. $N_{\theta}$ needs to satisfy $N_{\theta} > 1.5 L$.\paragraph{\tt ngrid\_zonal\_ctl}
\label{href_t:ngrid_zonal_ctl}
\verb|[Nphi]| \\
Number of grid in the zonal direction \verb|[Nphi]| is defined by integer.
Number of grid in the zonal direction $N_{\phi}$ is defined by integer [Nphi]. $N_{\phi}$ needs to satisfy $N_{\phi} = 2 N_{\theta}$.

\paragraph{\tt raidal\_grid\_type\_ctl}
\label{href_t:radial_grid_type_ctl}
\verb|[explicit, Chebyshev, or equi_distance]| \\
Type of the radial grid spacing is defined by text. The following types are supported in Calypso.
%
\begin{description}
\item{\tt explicit} Equi-distance grid
\item{\tt Chebyshev} Chebyshev collocation points
\item{\tt equi\_distance} Set explicitly by \verb|r_layer| array
\item{\tt equi\_distance} Equi-distance grid
\item{\tt explicit} Set explicitly by \verb|r_layer| array
\end{description}
%

Expand Down Expand Up @@ -224,12 +244,17 @@ \subsubsection{\tt num\_grid\_sph}
(This option works with \verb|radial_grid_type_ctl| is {\tt explicit} or {\tt Chebyshev}.)
Maximum radius of the domains \verb|[Rmax]| is defined by real. If this value is not defined, CMB becomes outer boundary of the domain.

\paragraph{\tt r\_layer}
\paragraph{\tt array r\_layer}
\label{href_t:r_layer}
\verb|[Layer #] [Radius]| \\
(This option works with \verb|[radial_grid_type_ctl]| is {\tt explicit}.)
List of the radial grid points in the simulation domain. Index of the radial point \verb|[Layer #]| is defined by integer, and radius \verb|[Radius]| is defined by real.

\paragraph{\tt array add\_external\_layer}
\label{href_t:add_external_layer}
\verb|[Radius]| \\
List of additional radial grid points. More grid points can be added in the Chebyshev or equi-distance grid. Radius of the additional points \verb|[Radius]| is defined by real.

\paragraph{\tt array boundaries\_ctl}
\verb|[Boundary_name] [Layer #]| \\
\label{href_t:boundaries_ctl}
Expand Down Expand Up @@ -296,7 +321,7 @@ \subsection{\tt phys\_values\_ctl}
\hline \hline
\tt viscous\_diffusion & Viscous diffusion
& $-\nu \nabla \times \nabla \times \bvec{u}$ \\
\tt inertia & Inertia term & $ \bvec{\omega} \times \bvec{u} $ \\
\tt inertia & Inertia term & $ -\bvec{\omega} \times \bvec{u} $ \\
\tt buoyancy & Thermal buoyancy & $ -\alpha_{T} T \bvec{g} $ \\
\tt composite\_buoyancy & Compositional buoyancy & $ -\alpha_{C} C\bvec{g} $\\
\tt Lorentz\_force & Lorentz force & $ \bvec{J} \times \bvec{B} $ \\
Expand Down Expand Up @@ -332,7 +357,7 @@ \subsection{\tt phys\_values\_ctl}
\begin{tabular}{|c|c|c|}
\hline
\tt [Name] & field name & Description \\ \hline \hline
\tt rot\_inertia & Curl of inertia & $ \nabla \times \left(\bvec{\omega} \times \bvec{u}\right) $ \\
\tt rot\_inertia & Curl of inertia & $ -\nabla \times \left(\bvec{\omega} \times \bvec{u}\right) $ \\
\tt rot\_Lorentz\_force & Curl of Lorentz force & $ \nabla \times \left(\bvec{J} \times \bvec{B}\right) $ \\
\tt rot\_Coriolis\_force & Curl of Coriolis force & $ -2 \Omega \nabla \times \left(\hat{z} \times \bvec{u} \right) $ \\
\tt rot\_buoyancy & Curl of thermal buoyancy & $ - \nabla \times \left(\alpha_{T} T \bvec{g}\right) $ \\
Expand Down
20 changes: 14 additions & 6 deletions doc/tex_src/install_CALYPSO.tex
Original file line number Diff line number Diff line change
Expand Up @@ -219,9 +219,10 @@ \subsubsection{Compile}
sph_add_initial_field* sph_mhd* tests/
sph_initial_field* sph_snapshot* utilities/
$ ls -F utilities/
assemble_sph* make_f90depends* t_ave_monitor_data*
field_to_VTK* sectioning* three_vizualizations*
gen_sph_grids* section_to_vtk*
./ field_to_VTK* sectioning*
../ gen_sph_grids* t_ave_monitor_data*
assemble_sph* make_f90depends* three_vizualizations*
check_control_mhd* section_to_vtk*
\end{verbatim}
%
%
Expand All @@ -241,6 +242,8 @@ \subsubsection{Compile}
\begin{description}
\item{\tt assemble\_sph: }\\
Data transfer program to change number of subdomains.
\item{\tt check\_control\_mhd: }\\
Quick check program for control data consistency.
\item{\tt gen\_sph\_grids: }\\
Preprocessing program for data transfer for spherical harmonics transform
\item{\tt t\_ave\_monitor\_data: }\\
Expand Down Expand Up @@ -306,20 +309,20 @@ \subsubsection{Distclean}
% make distclean
\end{verbatim}


\subsubsection{Install}
The executive files are copied to the install directory \verb|$(INSTDIR)/bin|. The install directory \verb|$(INSTDIR)| is defined in Makefile, and can also set by \verb|${--prefix}| option for \verb|configure| command. Alternatively, you can use the programs in \verb|${SRCDIR}/bin| directory without running \verb|make install|. If directory \verb|${PREFIX}| does not exist, \verb|make install | creates \verb|${PREFIX}|, \verb|${PREFIX}/lib|, \verb|${PREFIX}/bin|, and \verb|${PREFIX}/include| directories. No files are installed in \verb|${PREFIX}/lib| and \verb|${PREFIX}/include|.


\subsubsection{Construct dependecies (only for developper)}
The build process of Calypso consists of three steps:
Actual build process of Calypso by \verb|% make| consists of three steps:
%
\begin{enumerate}
\item Construct dependency of source files {\tt Makefile.depends} in each directory by {\tt make depends} command.
\item Construct {\tt Makefile} in {\tt [WORKDIR]} directory by {\tt make makemake} command.
\item Move into {\tt [WORKDIR]} and run {\tt make} command in {\tt [WORKDIR]} directory ({\tt cd [WORKDIR]; make})
\end{enumerate}
%
gmake supports parallel build by using {\tt -j [\# of process]} option, but the step 1 and 2 do not work correctly under the parallel build, but the step 3 (build under {\tt [WORKDIR} support the parallel build. Consequently, build time can be significantly reduced by run the step 3 sepalately with {\tt -j} option.
{\color{red} (Caution) Many large computer system does not recommend to use parallel build on the login nodes. Please check the computer center's documentations}

Fortran90 routines need to be build after modules which are used in the routines. C source files also need dependency among include files. Consequently, list of dependency of source files are saved in the file \verb|Makefile.depends| in each directory. When you modify the source files with changing the module usage, \verb|Makefile.depends| files need to be updated. To update the \verb|Makefile.depends|files, use the \verb|make| command at the \verb|[CALYPSO_HOME]| directory as \\
%
Expand All @@ -329,6 +332,11 @@ \subsubsection{Construct dependecies (only for developper)}

This process generate dependencies of the Fortran modules by program \verb|make_f90depends|. For C source files, the dependency is generated by the gcc with \verb|-MM -w -DDEPENDENCY_CHECK| option. Consequently, the dependencies need to be generated by the environment with gcc or compatible compiler. After generating the dependency, you can transfer the modified package and build without using gcc.

\subsection{Parallel build}
gmake supports parallel build by using {\tt -j [\# of process]} option. Calypso's build process supports purallel build. it may reduce the compile time. (We checked on Ubuntu and Mac OS.) \\
{\color{red} (Caution) Many large computer centers do not recommend to use parallel build on their login nodes. Please check the computer center's if you can use parallel builds}


\subsection{Install without using configure}
\label{section:no_configure}
It is possible to compile Calypso without using the \verb|configure| command. To do this, you need to edit the \verb|Makefile|. First, copy \verb|Makefile| from template \verb|Makefile.in| as
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