Fix dynamo benchmark cases 0 and 1 in examples

examples/dynamo_benchmark/dynamobench_case_0/README

@@ -6,26 +6,57 @@
  Here is the input files for the dynamo benchmark case 0.
 This example consists of the following files and directories
 
-control_MHD:        control file for simulation
-control_snapshot:   control file for data analysis
-control_resolution:  control file for spatial resolution
+control_MHD:         Control file for simulation
+control_snapshot:    Control file for data analysis
+control_mid_depth:   Control file for sectioning at mid-depth of the shell
 
-sph_lm31r48c_4:     Directory for spherical harmonics index table
-rst_4:              Directory for restart files
-field:              Directory for field data files
+sph_lm31r48c_4:      Directory for spherical harmonics index table
+rst_4:               Directory for restart files
+field:               Directory for field data files
+monitor:             Directory for time series data files
+sections:            Directory for field cross-section data files
 
-This example only run with 4 MPI processes. The simulation procedure is the following
+This example run with 4 MPI processes. The simulation procedure is the following
 
 1. Run simulation program
-[dynamobench_case_1]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_mhd
+[dynamobench_case_0]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_mhd
 
-2. To continue the simulation change rst_ctl in control_MHD from
+2. To continue the simulation Update the time stepping parameter 
+   "i_step_init_ctl" and "i_step_finish_ctl" in "time_step_ctl" block
+   to be the new start and end time steps, respectively.
+
+  And, change rst_ctl in control_MHD from
       rst_ctl                dynamo_benchmark_0
    to
       rst_ctl                start_from_rst_file
-   And, start simulation again by 2.
-
-4. To check the required results for dynamo benchmark, run 
-[dynamobench_case_1]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_dynamobench
+   And, start simulation again by procedure 1.
+
+   In the continuous runs, The time series data defined in "sph_monitor_ctl" block will be appended if time series data files are exist.
+
+
+3. The following data is written:
+    field/out.#.vtk.gz:  Visualization data for whole domain with gzipped VTK format
+    rst_4/rst.#.fst.gz:  Restart data with gzipped ASCII data merged over MPI processes
+    sections/equator.#.vtk.gz: Visualization data for equatorial plane with gzipped VTK format
+    sections/mid_depth.#.vtk: Visualization data for mid-depth of the fluid shell with VTK format
+
+    monitor/sph_ave_volume.dat:    Time series of volume average of fields.
+    monitor/sph_pwr_volume_s.dat:  Time series of mean square of fields.
+    monitor/sph_pwr_volume_l.dat:  Time series of mean square of spectr as a function of degree l
+    monitor/sph_pwr_volume_m.dat:  Time series of mean square of spectr as a function of order m
+    monitor/sph_pwr_volume_lm.dat: Time series of mean square of spectr as a function of (l-m)
+    monitor/sph_pwr_volume_m0.dat: Time series of mean square of axisymmetric components
+    monitor/dynamobench.dat:       Time series of required data for dynamo benchmark
+
+4. Required data for the benchmark is written in monitor/dynamobench.dat.
+The following data is written in each column.
+    t_step: Time step
+    time:   Time
+    KE_total: Average kinetic energy in the shell
+    v_phi:    $\phi$-component of the velocity at the requested point. (Average of the four requested points)
+   temperature: Temperature at the requested point. (Average of the four requested points)
+   Average_drift_vr: Drift frequency obtained by the position of the requested points (Average of the four requested points)
+   omega_vp44: Drift frequency obtained by l = |m| = 4 components of the poloidal velocity at the mid-depth.
+   omega_vt54: Drift frequency obtained by l = 5 and |m| = 4 components of the toroidal velocity at the mid-depth.
 
 

examples/dynamo_benchmark/dynamobench_case_0/control_MHD

@@ -259,13 +259,26 @@ begin MHD_control
   begin sph_monitor_ctl
     volume_average_prefix        'monitor/sph_ave_volume'
     volume_pwr_spectr_prefix     'monitor/sph_pwr_volume'
+    volume_pwr_spectr_format     'ASCII'
+!
+    begin dynamo_benchmark_data_ctl
+      dynamo_benchmark_file_prefix     'monitor/dynamobench'
+      dynamo_benchmark_file_format     'ASCII'
+      nphi_mid_eq_ctl                   512
+    end dynamo_benchmark_data_ctl
   end sph_monitor_ctl
 !
   begin visual_control
+!!!!!!!!! Parameters for sectioning module
     array cross_section_ctl
 !
+!!!!!!!!! Control parameters for mid-depth of the spherical shell
+      file  cross_section_ctl  'control_mid_depth'
+!
+!!!!!!!!! Control parameters for euqatorial plane
       begin cross_section_ctl
         section_file_prefix    'sections/equator'
+        psf_output_type        'VTK_gz'
 !
         begin surface_define
           section_method    plane
@@ -283,16 +296,14 @@ begin MHD_control
           end array center_position
 !
           array section_area_ctl
-            section_area_ctl   all   end
+            section_area_ctl   all
           end array section_area_ctl
         end surface_define
 !
         begin output_field_define
           array output_field
             output_field  temperature           scalar
-            output_field  velocity              vector
-            output_field  velocity              radial     
-            output_field  velocity              phi   
+            output_field  velocity              cyrindrical_vector
             output_field  vorticity             z
           end array output_field
         end output_field_define

examples/dynamo_benchmark/dynamobench_case_0/control_mid_depth

@@ -0,0 +1,34 @@
+!!!!!!!!! Control parameters for mid-depth of the spherical shell
+      file  cross_section_ctl  'control_mid_depth'
+!
+!!!!!!!!! Control parameters for euqatorial plane
+begin cross_section_ctl
+  section_file_prefix    'sections/mid_depth'
+  psf_output_type        'VTK'
+!
+  begin surface_define
+    section_method    sphere
+!
+    array center_position
+      center_position  x   0.0
+      center_position  y   0.0
+      center_position  z   0.0
+    end array center_position
+!
+    radius             1.0384
+!
+    array section_area_ctl
+      section_area_ctl   all
+    end array section_area_ctl
+  end surface_define
+!
+  begin output_field_define
+    array output_field
+      output_field  temperature           scalar
+      output_field  velocity              vector
+      output_field  velocity              radial     
+      output_field  velocity              phi   
+      output_field  vorticity             z
+    end array output_field
+  end output_field_define
+end cross_section_ctl

examples/dynamo_benchmark/dynamobench_case_0/sections/README

@@ -0,0 +1,6 @@
+!-----------------------------------------------------------------------
+!     Example using dynamo benchmark test Case 0
+!       Please see Christensen et.al. (2001) for the model description
+!-----------------------------------------------------------------------
+!
+ Time series data files are stored in this directory.

examples/dynamo_benchmark/dynamobench_case_1/README

@@ -6,26 +6,85 @@
  Here is the input files for the dynamo benchmark case 1 using 4 MPI processes.
 This example consists of the following files and directories
 
-control_MHD:        control file for simulation
-control_snapshot:   control file for data analysis
+control_MHD:          Control file for simulation
+control_snapshot:     Control file for data analysis
+control_resolution:   Control file for spatial resolution and parallelization
 
-sph_lm31r48c_4:     Directory for spherical harmonics index table
-rst_4:              Directory for restart files
-field:              Directory for field data files
+control_mid_depth:    Control file for sectioning at mid-depth of the shell
+control_CMB:          Control file for sectioning at the outer boundary of spherical chell
+control_equator:      Control file for sectioning at equatorial plane
+control_psf_z0.3:     Control file for sectioning at z = 0.3 (= 0.56 * r_i)
+control_psf_s0.55:    Control file for sectioning at a cylinder with s = 0.55 ( = 1.02 * r_i)
+control_zonal_mean:   Control file for sectioning at mid-depth of the shell
+control_iso_temp:     Control file for isosurface of temperature
 
-The simulation procedure is the following
+sph_lm31r48c_4:       Directory for spherical harmonics index table
+rst_4:                Directory for restart files
+field:                Directory for field data files
+monitor:              Directory for time series data files
+sections:             Directory for cross-section data files
+isosurfaces:          Directory for isosurface data files
 
-1: Run index generation program as
-[dynamobench_case_1]$ [CALYPSO_DIR]/bin/utilities/gen_sph_grids
+The parallelization information and initial field is built in the beginning of program. The simulation procedure is the following
 
-2. Generate initial field
-[dynamobench_case_1]$ [CALYPSO_DIR]/bin/sph_initial_field
-
-3. Run simulation program
+1. Run simulation program
 [dynamobench_case_1]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_mhd
 
-4. To check the required results for dynamo benchmark, run 
-[dynamobench_case_1]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_dynamobench
+2. To continue the simulation Update the time stepping parameter 
+   "i_step_init_ctl" and "i_step_finish_ctl" in "time_step_ctl" block
+   to be the new start and end time steps, respectively.
+
+  And, change rst_ctl in control_MHD from
+      rst_ctl                dynamo_benchmark_1
+   to
+      rst_ctl                start_from_rst_file
+   And, start simulation again by procedure 1.
+
+   In the continuous runs, The time series data defined in "sph_monitor_ctl" block will be appended if time series data files are exist.
+
+3. The following data is written:
+    field/out.#.vtk.gz:  Visualization data for whole domain with gzipped VTK format
+    rst_4/rst.#.fst.gz:  Restart data with gzipped ASCII data merged over MPI processes
+    sections/equator.#.vtk.gz: Visualization data for equatorial plane with gzipped VTK format
+    sections/mid_depth.#.vtk: Visualization data for mid-depth of the fluid shell with VTK format
+    sections/CMB.#.vtk.gz: Visualization data for equatorial plane with gzipped VTK format
+    sections/cylinder_s055.#.sdt: Visualization data for cylinder at s = 0.55 plane with bindary data format
+    sections/section_z03.#.sdt.gz: Visualization data for the plane at z = 0.3 with gzipped bindary data format
+
+    monitor/sph_ave_volume.dat:    Time series of volume average of fields.
+    monitor/sph_pwr_volume_s.dat:  Time series of mean square of fields.
+    monitor/sph_pwr_volume_l.dat:  Time series of mean square of spectr as a function of degree l
+    monitor/sph_pwr_volume_m.dat:  Time series of mean square of spectr as a function of order m
+    monitor/sph_pwr_volume_lm.dat: Time series of mean square of spectr as a function of (l-m)
+    monitor/sph_pwr_volume_m0.dat:      Time series of mean square of axisymmetric components
+    monitor/sph_pwr_layer_s.dat.gz:     Gzipped time series of mean square at 8-th and 16-th radial layers.
+    monitor/sph_pwr_layer_l.dat.gz:     Gzipped time series of mean square of spectr at 8-th and 16-th radial layers as a function of degree l
+    monitor/sph_pwr_layer_m.dat.gz:     Gzipped time series of mean square of spectr at 8-th and 16-th radial layers as a function of order m
+    monitor/sph_pwr_layer_lm.dat.gz:    Gzipped time series of mean square of spectr at 8-th and 16-th radial layers as a function of (l-m)
+    monitor/sph_pwr_layer_m0.dat.gz:    Gzipped time series of mean square of axisymmetric components at 8-th and 16-th radial layers
+    monitor/picked_mode_l1_m0c.dat.gz:  Gzipped time series of spherical harmonic coefficients at l=1 and m = 0.
+    monitor/picked_mode_l2_m0c.dat.gz:  Gzipped time series of spherical harmonic coefficients at l=2 and m = 0.
+    monitor/gauss_coefs.dat:            Time series of Gauss coefficients
+    monitor/dipolarity.dat.gz:          Gzipped time series of dipolarities with various truncations
+    monitor/Nusselt.dat.gz:             Gzipped time series of the Nusselt number at the both boundaries.
+    monitor/dynamobench.dat:            Time series of required data for dynamo benchmark
 
-Enjoy!!
+4. Required data for the benchmark is written in monitor/dynamobench.dat.
+The following data is written in each column.
+    t_step: Time step
+    time:   Time
+    KE_total: Average kinetic energy in the shell
+    ME_total: Average kinetic energy in the shell
+    v_phi:    $\phi$-component of the velocity at the requested point. (Average of the four requested points)
+    B_theta:  $\theta$-component of the magnetic field at the requested point. (Average of the four requested points)
+   temperature: Temperature at the requested point. (Average of the four requested points)
+   Average_drift_vr: Drift frequency obtained by the position of the requested points (Average of the four requested points)
+   omega_vp44: Drift frequency obtained by l = |m| = 4 components of the poloidal velocity at the mid-depth.
+   omega_vt54: Drift frequency obtained by l = 5 and |m| = 4 components of the toroidal velocity at the mid-depth.
 
+5. Data conversion for cross sections.
+ Cross section data for the cylinder at s = 0.55 and the plane at z = 0.3 are saved by the (gzipped) bindary format. The program "field_to_VTK" in "bin/utilities" folder can convert these data into VTK format. "field_to_VTK" is a serial program, so it can start by 
+
+[dynamobench_case_1]$ [CALYPSO_DIR]/bin/utilities/field_to_VTK
+
+

examples/dynamo_benchmark/dynamobench_case_1/control_psf_CMB → examples/dynamo_benchmark/dynamobench_case_1/control_CMB

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

examples/dynamo_benchmark/dynamobench_case_1/control_MHD

@@ -266,8 +266,8 @@ begin MHD_control
 !
 !!!!!  control for restart data
     begin restart_file_ctl
-!      rst_ctl                dynamo_benchmark_1
-      rst_ctl                start_from_rst_file
+      rst_ctl                dynamo_benchmark_1
+!      rst_ctl                start_from_rst_file
     end restart_file_ctl
 !
 !!!!!!   method for time evolution
@@ -285,10 +285,14 @@ begin MHD_control
 begin sph_monitor_ctl
     volume_average_prefix        'monitor/sph_ave_volume'
     volume_pwr_spectr_prefix     'monitor/sph_pwr_volume'
-    nusselt_number_prefix        'monitor/Nusselt'
+    volume_pwr_spectr_format     'ASCII'
+!
+	nusselt_number_prefix        'monitor/Nusselt'
+    nusselt_number_format        'gzip'
 !
     begin layered_spectrum_ctl
       layered_pwr_spectr_prefix    'monitor/sph_pwr_layer'
+      layered_pwr_spectr_format    'gzip'
 !
        array spectr_layer_ctl
          spectr_layer_ctl  1
@@ -299,6 +303,7 @@ begin sph_monitor_ctl
 !
     begin pickup_spectr_ctl
       picked_sph_prefix     'monitor/picked_mode'
+      picked_sph_format     'gzip'
 !
       array pick_layer_ctl
         pick_layer_ctl    8
@@ -319,18 +324,28 @@ begin sph_monitor_ctl
         pick_gauss_coef_degree_ctl   1
       end array pick_gauss_coef_degree_ctl
     end gauss_coefficient_ctl
+!
+    begin sph_dipolarity_ctl
+      dipolarity_file_prefix        'monitor/dipolarity'
+      dipolarity_file_format        'gzip'
+
+      array dipolarity_truncation_ctl
+        dipolarity_truncation_ctl     13
+      end array dipolarity_truncation_ctl
+    end sph_dipolarity_ctl
 !
     begin dynamo_benchmark_data_ctl
       dynamo_benchmark_file_prefix     'monitor/dynamobench'
-      dynamo_benchmark_file_format     'gzip'
+      dynamo_benchmark_file_format     'ASCII'
       nphi_mid_eq_ctl                   512
     end dynamo_benchmark_data_ctl
   end sph_monitor_ctl
 !
   begin visual_control
     array cross_section_ctl
-      file  cross_section_ctl   control_psf_CMB
-      file  cross_section_ctl   control_psf_eq 
+      file  cross_section_ctl   control_mid_depth
+      file  cross_section_ctl   control_CMB
+      file  cross_section_ctl   control_equator 
       file  cross_section_ctl   control_psf_z0.3
       file  cross_section_ctl   control_psf_s0.55
     end array cross_section_ctl
@@ -340,7 +355,7 @@ begin sph_monitor_ctl
     end array isosurface_ctl
   end  visual_control
 !
-  begin dynamo vizs control
-    file zonal mean section ctl  control_psf_zm
-  end dynamo vizs control
+  begin dynamo_vizs_control
+    file zonal_mean_section_ctl  control_zonal_mean
+  end dynamo_vizs_control
 end MHD_control

examples/dynamo_benchmark/dynamobench_case_1/control_psf_eq → examples/dynamo_benchmark/dynamobench_case_1/control_equator

@@ -3,6 +3,7 @@
 !
 begin cross_section_ctl
   section_file_prefix    'sections/equator'
+  psf_output_type         VTK_gz
 !
   begin surface_define
     section_method    equation

examples/dynamo_benchmark/dynamobench_case_1/control_iso_temp

@@ -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_1/control_mid_depth

@@ -0,0 +1,33 @@
+!!!!!!!!! Control parameters for mid-depth of the spherical shell
+      file  cross_section_ctl  'control_mid_depth'
+!
+!!!!!!!!! Control parameters for euqatorial plane
+begin cross_section_ctl
+  section_file_prefix    'sections/mid_depth'
+  psf_output_type        'VTK'
+!
+  begin surface_define
+    section_method    sphere
+!
+    array center_position
+      center_position  x   0.0
+      center_position  y   0.0
+      center_position  z   0.0
+    end array center_position
+!
+    radius             1.0384
+!
+    array section_area_ctl
+      section_area_ctl   all
+    end array section_area_ctl
+  end surface_define
+!
+  begin output_field_define
+    array output_field
+      output_field  temperature           scalar
+      output_field  velocity              sphrical_vector
+      output_field  vorticity             z
+      output_field  magnetic_field        sphrical_vector
+    end array output_field
+  end output_field_define
+end cross_section_ctl