[cig-commits] [commit] master, python-removal, rajesh-petsc-schur: Updated Cookbook 4 in the CitcomS manual to the pure C version. Removed parameters with default values from cookbook4 in the examples/Cookbook4 directory (5a0eadf)

cig_noreply at geodynamics.org cig_noreply at geodynamics.org
Wed Nov 5 19:02:04 PST 2014 

Repository : https://github.com/geodynamics/citcoms

On branches: master,python-removal,rajesh-petsc-schur
Link       : https://github.com/geodynamics/citcoms/compare/464e1b32299b15819f93efd98d969cddb84dfe51...f97ae655a50bdbd6dac1923a3471ee4dae178fbd

>---------------------------------------------------------------

commit 5a0eadfd7ff11a7494442933abf87f58cbb2efee
Author: Rajesh Kommu <rajesh.kommu at gmail.com>
Date:   Wed Jun 25 16:11:59 2014 -0700

    Updated Cookbook 4 in the CitcomS manual to the pure C version. Removed
    parameters with default values from cookbook4 in the examples/Cookbook4
    directory


>---------------------------------------------------------------

5a0eadfd7ff11a7494442933abf87f58cbb2efee
 doc/citcoms-manual.pdf       | Bin 10838838 -> 10838652 bytes
 doc/citcoms-manual.tex       | 104 ++++++++++++-------------
 examples/Cookbook4/cookbook4 | 182 +------------------------------------------
 3 files changed, 55 insertions(+), 231 deletions(-)

diff --git a/doc/citcoms-manual.pdf b/doc/citcoms-manual.pdf
index 91a1043..30438fc 100644
Binary files a/doc/citcoms-manual.pdf and b/doc/citcoms-manual.pdf differ
diff --git a/doc/citcoms-manual.tex b/doc/citcoms-manual.tex
index 5ae646d..c7c1626 100644
--- a/doc/citcoms-manual.tex
+++ b/doc/citcoms-manual.tex
@@ -2711,67 +2711,67 @@ while a lower resolution is sufficient for the wider cold downwelling.
 \subsection{Solution}
 
 The parameter that controls whether a mesh is to be uniform or refined
-is \texttt{solver.mesher.coor}. Set it to \texttt{1} \texttt{(solver.mesher.coor=1)}
+is \texttt{coor}. Set it to \texttt{1} \texttt{(coor=1)}
 in order to read the uneven mesh point coordinates from an input file
 (specified by \texttt{coor\_file}). The format of the coordinate input
 file is described in Appendix \vref{sec:Coordinate-files}.
 \begin{lyxcode}
-coor~=~1~\\
-coor\_file~=~coor.dat
+coor=1\\
+coor\_file=coor.dat
 \end{lyxcode}
 The computational domain is bounded in colatitude between radian 1
 and 2, in latitude between radian 0 and 1, and in radius between 0.55
 and 1, as determined by the content of \texttt{coor\_file}.
 
 
-\subsubsection{Example: Regionally Refined Meshes, \texttt{cookbook4.cfg}}
-\begin{lyxcode}
-{[}CitcomS{]}~\\
-steps~=~250~~~~~~~~~~~~~~~~~;~number~of~time~steps~\\
-~\\
-{[}CitcomS.controller{]}~\\
-monitoringFrequency~=~10~~~~;~how~often~outputs~are~created~\\
-~\\
-{[}CitcomS.solver{]}~\\
-rayleigh~=~1e6~~~~~~~~~~~~~~;~Rayleigh~number~\\
-datafile~=~cookbook4~~~~~~~~;~prefix~of~output~filenames~\\
-~\\
-{[}CitcomS.solver.ic{]}~\\
-num\_perturbations~=~1~\\
-perturbmag~=~0.05~\\
-perturblayer~=~10~\\
-~\\
-\#~Perturb~the~initial~temperature~gradient~in~the~longitudinal~\\
-\#~direction.~\\
-perturbl~=~1~\\
-perturbm~=~0~\\
-~\\
-{[}CitcomS.solver.mesher{]}~\\
-\#~Read~uneven~mesh~point~coordinates~from~'coor.dat'.~\\
-coor~=~1~\\
-coor\_file~=~coor.dat~\\
-~\\
-nprocx~=~2~\\
-nprocy~=~1~\\
-nprocz~=~1~\\
-nodex~=~33~\\
-nodey~=~17~\\
-nodez~=~17~\\
-~\\
-{[}CitcomS.solver.visc{]}~\\
-VISC\_UPDATE~=~on~\\
-num\_mat~=~4~\\
-visc0~=~1,1,1,1~\\
-TDEPV~=~on~\\
-rheol~=~4~\\
-viscE~=~0.2,0.2,0.2,0.2~\\
-viscT~=~0,0,0,0~\\
-viscZ~=~0,0,0,0~\\
-VMIN~=~on~\\
-visc\_min~=~1.0~\\
-VMAX~=~on~\\
-visc\_max~=~100.0
-\end{lyxcode}
+\subsubsection{Example: Regionally Refined Meshes, \texttt{cookbook4}}
+\begin{verbatim}
+# CitcomS
+cpu_limits_in_seconds=360000000
+minstep=250
+
+# CitcomS.controller
+storage_spacing=50
+
+# CitcomS.solver
+datafile=cookbook4
+rayleigh=1e6
+
+# CitcomS.solver.mesher
+coor=1
+coor_file=coor.dat
+fi_max=1
+fi_min=0
+nodex=33
+nodey=17
+nodez=17
+nprocx=1
+nprocy=1
+nprocz=1
+theta_max=2.0708
+theta_min=1.0708
+
+# CitcomS.solver.ic
+num_perturbations=1
+perturbl=1
+perturblayer=10
+perturbm=0
+perturbmag=0.05
+
+# CitcomS.solver.visc
+TDEPV=on
+VISC_UPDATE=on
+VMAX=on
+VMIN=on
+num_mat=4
+rheol=4
+visc0=1,1,1,1
+viscE=0.2,0.2,0.2,0.2
+viscT=0,0,0,0
+viscZ=0,0,0,0
+visc_max=100.0
+visc_min=1.0
+\end{verbatim}
 \begin{figure}[H]
 \begin{centering}
 \includegraphics{graphics/cookbook4.pdf}
@@ -2885,7 +2885,7 @@ so the Euler pole moved closer.}
 
 
 
-\subsubsection{Example: Subduction Models with Trench Rollback, \texttt{cookbook5.cfg}}
+\subsubsection{Example: Subduction Models with Trench Rollback, \texttt{cookbook5}}
 \begin{verbatim}
 # CitcomS
 cpu_limits_in_seconds=360000000
diff --git a/examples/Cookbook4/cookbook4 b/examples/Cookbook4/cookbook4
index 2409a64..e0a63a3 100644
--- a/examples/Cookbook4/cookbook4
+++ b/examples/Cookbook4/cookbook4
@@ -1,222 +1,46 @@
 # CitcomS
 cpu_limits_in_seconds=360000000
-maxstep=1000
-maxtotstep=1000000
 minstep=250
-solver=regional
 
 # CitcomS.controller
-checkpointFrequency=100
 storage_spacing=50
 
 # CitcomS.solver
-Q0=0
-datadir="cb4output"
-datadir_old="."
 datafile=cookbook4
-datafile_old="regtest"
-dissipation_number=0.0
-gruneisen=0.0
 rayleigh=1e6
-see_convergence=1
-stokes_flow_only=0
-surfaceT=0.1
-verbose=0
 
 # CitcomS.solver.mesher
 coor=1
 coor_file=coor.dat
-coor_refine=0.1,0.15,0.1,0.2
 fi_max=1
 fi_min=0
-levels=1
-mgunitx=8
-mgunity=8
-mgunitz=8
 nodex=33
 nodey=17
 nodez=17
-nproc_surf=1
-nprocx=4
-nprocy=2
-nprocz=2
-nr=1
-r_grid_layers=1
-radius_inner=0.55
-radius_outer=1
-rr=1
+nprocx=1
+nprocy=1
+nprocz=1
 theta_max=2.0708
 theta_min=1.0708
 
-# CitcomS.solver.tsolver
-ADV=1
-adv_gamma=0.5
-adv_sub_iterations=2
-filter_temp=0
-finetunedt=0.9
-fixed_timestep=0.0
-input_diffusivity=1
-inputdiffusivity=1
-monitor_max_T=1
-
-# CitcomS.solver.vsolver
-Solver=cgrad
-accuracy=1.0e-4
-aug_lagr=1
-aug_number=2000
-check_continuity_convergence=1
-check_pressure_convergence=1
-compress_iter_maxstep=100
-down_heavy=3
-inner_accuracy_scale=1.0
-inner_remove_rigid_rotation=0
-max_mg_cycles=50
-mg_cycle=1
-node_assemble=1
-only_check_vel_convergence=0
-piterations=1000
-precond=1
-remove_angular_momentum=1
-remove_rigid_rotation=1
-up_heavy=3
-uzawa=cg
-vhighstep=3
-vlowstep=1000
-
-# CitcomS.solver.bc
-bottbc=1
-bottbcval=1
-botvbc=0
-botvbxval=0
-botvbyval=0
-depth_bound_adj=0.157
-pseudo_free_surf=0
-side_sbcs=0
-temperature_bound_adj=0
-toptbc=1
-toptbcval=0
-topvbc=0
-topvbxval=0
-topvbyval=0
-width_bound_adj=0.08727
-
-# CitcomS.solver.const
-cp=1200
-density=3340.0
-density_above=1030.0
-density_below=6600.0
-gravacc=9.81
-radius=6.371e+06
-refvisc=1e+21
-thermdiff=1e-06
-thermexp=3e-05
-z_410=0.06435
-z_cmb=0.439
-z_lith=0.014
-z_lmantle=0.105
-
 # CitcomS.solver.ic
-blob_center=[-999,-999,-999]
-blob_dT=0.18
-blob_radius=0.063
-half_space_age=40
-mantle_temp=1.0
 num_perturbations=1
 perturbl=1
 perturblayer=10
 perturbm=0
 perturbmag=0.05
-post_p=0
-restart=0
-solution_cycles_init=0
-tic_method=0
-zero_elapsed_time=1
-
-# CitcomS.solver.output
-cache_mdc_nelmts=10330
-cache_rdcc_nbytes=1048576
-cache_rdcc_nelmts=521
-cb_block_size=1048576
-cb_buffer_size=4194304
-gzdir_rnr=0
-gzdir_vtkio=1
-output_alignment=262144
-output_alignment_threshold=524288
-output_format="ascii"
-output_ll_max=20
-output_optional="surf,botm,tracer"
-self_gravitation=0
-sieve_buf_size=1048576
-use_cbf_topo=0
-vtk_format=binary
-write_q_files=0
-
-# CitcomS.solver.param
-file_tbcs=0
-file_vbcs=0
-lith_age=0
-lith_age_depth=0.0314
-lith_age_file="age.dat"
-lith_age_time=0
-mat_control=0
-mat_file="mat.dat"
-mineral_physics_model=3
-reference_state=1
-refstate_file="refstate.dat"
-reset_startage=0
-start_age=40
-temp_bound_file=btemp.dat
-vel_bound_file="bevel.dat"
-
-# CitcomS.solver.phase
-Ra_410=0
-Ra_670=0
-Ra_cmb=0
-clapeyron410=0.0235
-clapeyron670=-0.0235
-clapeyroncmb=-0.0235
-transT410=0.78
-transT670=0.78
-transTcmb=0.875
-width410=0.0058
-width670=0.0058
-widthcmb=0.0058
-
-# CitcomS.solver.tracer
 
 # CitcomS.solver.visc
-CDEPV=0
-PDEPV=0
-SDEPV=0
 TDEPV=on
 VISC_UPDATE=on
 VMAX=on
 VMIN=on
-Viscosity="system"
-cdepv_ff=1,1
-low_visc_channel=0
-low_visc_wedge=0
-lv_channel_thickness=0.0047
-lv_max_radius=0.9921
-lv_min_radius=0.9764
-lv_reduction=0.5
 num_mat=4
-pdepv_a=1e20,1e20,1e20,1e20
-pdepv_b=0,0,0,0
-pdepv_eff=1
-pdepv_offset=0
-pdepv_y=1e20,1e20,1e20,1e20
 rheol=4
-sdepv_expt=1,1,1,1
-sdepv_misfit=0.001
 visc0=1,1,1,1
 viscE=0.2,0.2,0.2,0.2
 viscT=0,0,0,0
 viscZ=0,0,0,0
-visc_layer_control=0
-visc_layer_file=visc.dat
 visc_max=100.0
 visc_min=1.0
-visc_smooth_method=3
-z_layer=-999,-999,-999,-999

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