Change section data file format flag for controls and depreacted control labels in tests and examples

Author: hiromatsui

doc/CALYPSO.pdf

@@ -1275,8 +1275,8 @@ \subsection{\tt cross\_section\_ctl}
 \verb|[file_prefix]| \\
 File prefix for cross section data is defined as character \verb|[file_prefix]|.
 
-\paragraph{\tt psf\_output\_type}
-\label{href_t:psf_output_type}
+\paragraph{{\tt section\_file\_format} or {\tt psf\_output\_type}}
+\label{href_t:section_file_format}
 \verb|[file_format]| \\
 File format for cross section data is defined as character \verb|[file_format]|. The following formats are available;
 \begin{description}

doc/tex_src/controls_CALYPSO.tex

@@ -1062,8 +1062,10 @@ \subsection{Cross section data (Parallel Surfacing module)}
 \begin{itemize}
 	\item \hyperref[href_t:section_file_prefix]
 			{\tt section\_file\_prefix    [section\_prefix]}
-	\item \hyperref[href_t:psf_output_type]
-			{\tt psf\_output\_type        [file\_format]}
+	\item \hyperref[href_t:section_file_format]
+			{\tt section\_file\_format        [file\_format]}
+    \item \hyperref[href_t:psf_output_type]
+            {\tt psf\_output\_type        [file\_format]}         {\color{red}(Deprecated)}
 	\item File or Block \hyperref[href_t:surface_define]{\tt surface\_define    [File\_Name]}
 		\begin{itemize}
 			\item \hyperref[href_t:section_method]
@@ -1091,7 +1093,7 @@ \subsection{Cross section data (Parallel Surfacing module)}
 
 \paragraph{Output data format of sectioning module}
 \label{sec:PSF_data}
-Sectioning data are written with VTK format and VTK data compressed by zlib. Field data also output by binary format and binary compressed by zlib. The list of data format and control flag for \verb|psf_output_type| are listed in Table \ref{table:PSF_data}. In the binary data format, position data and field data are saved independently not to write the grid data for each output step. Program \hyperref[section:section_to_VTK]{\tt section\_to\_VTK} generates VTK file from the binary section data. The output data format is defined by \verb|psf_output_type|. Because the field data is written by using Cartesian coordinate $(x,y,z)$ system, $(x,y,z)$ components in ParaView corresponds to the spherical components $(r, \theta, \phi)$ or cylindrical componennts $(s,\phi, z)$ if sectioning data is writtein the spherical or cylindrical componnents. Consequently, ParaView can not draw griph or field lines for these spherical or cylindrical vectors.
+Sectioning data are written with VTK format and VTK data compressed by zlib. Field data also output by binary format and binary compressed by zlib. The list of data format and control flag for \verb|section_file_format| are listed in Table \ref{table:PSF_data}. In the binary data format, position data and field data are saved independently not to write the grid data for each output step. Program \hyperref[section:section_to_VTK]{\tt section\_to\_VTK} generates VTK file from the binary section data. The output data format is defined by \verb|section_file_format|. Because the field data is written by using Cartesian coordinate $(x,y,z)$ system, $(x,y,z)$ components in ParaView corresponds to the spherical components $(r, \theta, \phi)$ or cylindrical componennts $(s,\phi, z)$ if sectioning data is writtein the spherical or cylindrical componnents. Consequently, ParaView can not draw griph or field lines for these spherical or cylindrical vectors.
 %
 \begin{table}[htp]
 \caption{Data format  and an example of data size and output time  for sectioning data}

doc/tex_src/programs_CALYPSO.tex

@@ -20,11 +20,11 @@ begin MHD_control
     debug_flag_ctl            'Off'
 !
     num_subdomain_ctl            4
-    num_smp_ctl                  2
+    num_smp_ctl                  4
 !
     restart_file_prefix         'rst_4/rst'
     field_file_prefix           'field/out'
-    restart_file_fmt_ctl       'merged_gz'
+    restart_file_fmt_ctl       'merged_bin_gz'
     field_file_fmt_ctl         'merged_VTK_gz'
   end data_files_def
 !
@@ -52,7 +52,7 @@ begin MHD_control
 !
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !
-  file spherical_shell_ctl  'control_resolution'
+  file spherical_shell_ctl  'sph_lm63r72c_ic_6/control_resolution'
 !
   begin model
 !!!!!  physical values!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -119,8 +119,8 @@ begin MHD_control
       end array bc_velocity
 !
       array bc_magnetic_field
-        bc_magnetic_field  sph_to_center  to_Center  0.000  end
-        bc_magnetic_field  insulator      CMB        0.000  end
+        bc_magnetic_field  sph_to_center  to_Center  0.000
+        bc_magnetic_field  insulator      CMB        0.000
       end array bc_magnetic_field
     end boundary_condition
 !
@@ -344,19 +344,19 @@ begin MHD_control
 !
   begin visual_control
     array cross_section_ctl
-      file  cross_section_ctl   control_psf_CMB
-      file  cross_section_ctl   control_psf_ICB
-      file  cross_section_ctl   control_psf_eq 
-      file  cross_section_ctl   control_psf_z0.3
-      file  cross_section_ctl   control_psf_s0.55
+      file  cross_section_ctl   controls/control_psf_CMB
+      file  cross_section_ctl   controls/control_psf_ICB
+      file  cross_section_ctl   controls/control_psf_eq 
+      file  cross_section_ctl   controls/control_psf_z0.3
+      file  cross_section_ctl   controls/control_psf_s0.55
     end array cross_section_ctl
 !
     array isosurface_ctl
-      file  isosurface_ctl      control_iso_temp
+      file  isosurface_ctl      controls/control_iso_temp
     end array isosurface_ctl
   end  visual_control
 !
   begin dynamo vizs control
-    file zonal mean section ctl  control_psf_zm
+    file zonal mean section ctl  controls/control_psf_zm
   end dynamo vizs control
 end MHD_control

examples/dynamo_benchmark/dynamobench_case_2/control_MHD

@@ -1,6 +1,7 @@
 !
 begin isosurface_ctl
-  isosurface_file_prefix    'Isosurfaces/temp0_7'
+  isosurface_file_prefix    'isosurfaces/temp0_7'
+  iso_output_type            vtk_gz
 !
   begin isosurf_define
     isosurf_field        temperature

examples/dynamo_benchmark/dynamobench_case_2/control_resolution

@@ -4,6 +4,7 @@
 !
 begin cross_section_ctl
   section_file_prefix    'sections/CMB'
+  section_file_format    'VTK_gz'
 !
   begin surface_define
     section_method    sphere

examples/dynamo_benchmark/dynamobench_case_2/control_iso_temp renamed to examples/dynamo_benchmark/dynamobench_case_2/controls/control_iso_temp

@@ -4,6 +4,7 @@
 !
 begin cross_section_ctl
   section_file_prefix    'sections/ICB'
+  section_file_format    'VTK_gz'
 !
   begin surface_define
     section_method    sphere

examples/dynamo_benchmark/dynamobench_case_2/control_psf_CMB renamed to examples/dynamo_benchmark/dynamobench_case_2/controls/control_psf_CMB

@@ -3,6 +3,7 @@
 !
 begin cross_section_ctl
   section_file_prefix    'sections/equator'
+  section_file_format    'VTK'
 !
   begin surface_define
     section_method    plane

examples/dynamo_benchmark/dynamobench_case_2/control_psf_ICB renamed to examples/dynamo_benchmark/dynamobench_case_2/controls/control_psf_ICB

@@ -4,6 +4,7 @@
 !
 begin cross_section_ctl
   section_file_prefix    'sections/cylinder_s055'
+  section_file_format    'PSF'
 !
   begin surface_define
     section_method    ellipsoid