[cig-commits] r14776 - doc/CitcomS/manual

tan2 at geodynamics.org tan2 at geodynamics.org
Mon Apr 20 12:54:38 PDT 2009


Author: tan2
Date: 2009-04-20 12:54:38 -0700 (Mon, 20 Apr 2009)
New Revision: 14776

Modified:
   doc/CitcomS/manual/citcoms.lyx
Log:
Updated the description of input parameters, esp. new parameters: mineral_physics_model, self_gravitation, use_cbf_topo, remove_angular_momentum, max_mg_cycles; and available schedulers.


Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx	2009-04-20 18:27:43 UTC (rev 14775)
+++ doc/CitcomS/manual/citcoms.lyx	2009-04-20 19:54:38 UTC (rev 14776)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 276
 \begin_document
 \begin_header
@@ -11119,21 +11119,21 @@
 
 .
  A tetrahedral symmetric pattern is developed for the convection.
- The surface heatflux 
+ The surface heat flux 
 \begin_inset Formula $H_{surf}$
 \end_inset
 
- at the steady state is 3.892, and the bottom heatflux 
+ at the steady state is 3.892, and the bottom heat flux 
 \begin_inset Formula $H_{botm}$
 \end_inset
 
  is 12.817.
- The heatflux imbalance (
+ The heat flux imbalance (
 \begin_inset Formula $H_{botm}r_{inner}^{2}/H_{surf}r_{outer}^{2}-1$
 \end_inset
 
 ) is -0.38%.
- The Nussult number, converted from Equation 
+ The Nussult number, converted from the surface heat flux by Equation 
 \begin_inset LatexCommand ref
 reference "eq:Nusselt number"
 
@@ -11564,8 +11564,8 @@
 0.2
 \family default
 ) too high.
- This can cause the mesh size to change too rapidly across an element and
- the temperature solver to generate pronounced numerical artifacts.
+ This can cause the mesh size to change too rapidly across an element, which
+ will generate pronounced numerical artifacts in the temperature solver.
 \end_layout
 
 \begin_layout LyX-Code
@@ -11709,8 +11709,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.ccoupler]
 \newline
 two_way_communication = on
@@ -11720,8 +11718,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.ecoupler]
 \newline
 two_way_communication = on
@@ -11735,8 +11731,6 @@
 \newline
 
 \newline
-
-\newline
 # assigning processors
  to csolver and esolver
 \newline
@@ -11749,16 +11743,12 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.ccontroller]
 \newline
 monitoringFrequency = 2
 \newline
 
 \newline
-
-\newline
 [CitcomS.econtroller]
 \newline
 monitorin
@@ -11766,8 +11756,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.csolver]
 \newline
 datadir_old = ic
@@ -11783,8 +11771,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.csolver.mesher]
 \newline
 nprocz = 2
@@ -11815,8 +11801,6 @@
 \newline
 
 \newline
-
-\newline
 [Cit
 comS.csolver.bc]
 \newline
@@ -11824,8 +11808,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.csolver.param]
 \newline
 file_vbcs = on
@@ -11837,8 +11819,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.csolver.ic]
 \newline
 tic_method = -1
@@ -11848,8 +11828,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.csolver.tsolver]
 \newline
 ADV = on
@@ -11870,57 +11848,44 @@
 \newline
 
 \newline
-
-\newline
-[CitcomS.csolver.vsolver]
-\newline
-tole_compressibility = 8e-6
-\newline
-
-\newline
-
-\newline
 [CitcomS.csolver.visc]
 \newline
-VISC_UPD
-ATE = on
+VISC_UPDATE = on
 \newline
 num_mat = 4
 \newline
 visc0 = 1,1,1,1
 \newline
-TDEPV = on
+TDEPV =
+ on
 \newline
 viscE = 1.6,1.6,1.6,1.6
 \newline
 viscT = 0,0,0,0
 \newline
-VM
-IN = on
+VMIN = on
 \newline
 visc_min = 1.0
 \newline
 VMAX = on
 \newline
-visc_max = 100.0
+visc_max
+ = 100.0
 \newline
 
 \newline
-
+###############################################
 \newline
-####################################
-###########
-\newline
 
 \newline
 [CitcomS.esolver]
 \newline
-datadir_old = ic
+datadir_ol
+d = ic
 \newline
 datafile_old = embd
 \newline
-datadir =
- output
+datadir = output
 \newline
 datafile = embd
 \newline
@@ -11928,14 +11893,12 @@
 \newline
 
 \newline
-
+[CitcomS.es
+olver.mesher]
 \newline
-[CitcomS.esolver.mesher]
-\newline
 nprocz = 2
 \newline
-nodex
- = 21
+nodex = 21
 \newline
 nodey = 21
 \newline
@@ -11943,10 +11906,10 @@
 \newline
 radius_outer = 0.999
 \newline
-radius_inner = 0.551
+radius_in
+ner = 0.551
 \newline
-theta_min
- = 1.421
+theta_min = 1.421
 \newline
 theta_max = 1.721
 \newline
@@ -11956,55 +11919,41 @@
 \newline
 
 \newline
-
+[CitcomS.esolve
+r.ic]
 \newline
-[CitcomS.esolver.ic]
+tic_method = -1
 \newline
-tic_method
- = -1
-\newline
 solution_cycles_init = 0
 \newline
 
 \newline
-
-\newline
-[CitcomS.esolver.vsolver]
-\newline
-tole_compressibility
- = 6e-6
-\newline
-
-\newline
-
-\newline
 [CitcomS.esolver.tsolver]
 \newline
-ADV = on
+ADV =
+ on
 \newline
 filter_temp = off
 \newline
 monitor_max_T = off
 \newline
-finetu
-nedt = 0.9
+finetunedt = 0.9
 \newline
 fixed_timestep = 0
 \newline
-adv_gamma = 0.5
+adv_gamm
+a = 0.5
 \newline
 adv_sub_iterations = 2
 \newline
 
 \newline
-
+[CitcomS.esolver.visc]
 \newline
-[CitcomS.esolver.vi
-sc]
-\newline
 VISC_UPDATE = on
 \newline
-num_mat = 4
+num_mat
+ = 4
 \newline
 visc0 = 1,1,1,1
 \newline
@@ -12012,12 +11961,12 @@
 \newline
 viscE = 1.6,1.6,1.6,1.6
 \newline
-viscT
- = 0,0,0,0
+viscT = 0,0,0,0
 \newline
 VMIN = on
 \newline
-visc_min = 1.0
+visc_min
+ = 1.0
 \newline
 VMAX = on
 \newline
@@ -12025,12 +11974,9 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.esolver.bc]
 \newline
-side_s
-bcs = on
+side_sbcs = on
 \end_layout
 
 \begin_layout Subsection
@@ -12201,54 +12147,16 @@
 
 \family typewriter
 \size small
-file_vbcs=off
-\newline
-vel_bound_file="bvel.dat"
+mineral_physics_model=3
 \end_layout
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Standard
-If 
-\family typewriter
-\size small
-file_vbcs
-\family default
-\size default
- is set to 
-\family typewriter
-\size small
-on
-\family default
-\size default
-, the top surface velocity boundary conditions are read in from files which
- have location and name specified by 
-\family typewriter
-\size small
-vel_bound_file
-\size default
-.
-
-\family default
- Requires setting 
-\family typewriter
-\size small
-topvbc=1
-\family default
-\size default
- to take effect.
- If you wish to have a uniform top surface velocity boundary condition or
- some simple geometric pattern, then 
-\family typewriter
-\size small
-file_vbcs
-\family default
-\size default
- should be set to zero.
- 
+Using which mineral physics model to convert the seismic velocities.
 \end_layout
 
 \end_inset
@@ -12262,17 +12170,9 @@
 
 \family typewriter
 \size small
-coor=0
-\family default
-\size default
-
+file_vbcs=off
 \newline
-
-\family typewriter
-\size small
-coor_file="coor.dat"
-\newline
-coor_refine=0.1,0.15,0.1,0.2
+vel_bound_file="bvel.dat"
 \end_layout
 
 \end_inset
@@ -12283,56 +12183,41 @@
 \begin_layout Standard
 If 
 \family typewriter
-coor
+\size small
+file_vbcs
 \family default
- is set to 0, then there will be uniform mesh in the latitudinal, longitudinal,
- and radial directions.
- If you wish to have a regular but uneven spacing between elements, 
+\size default
+ is set to 
 \family typewriter
-coor
-\family default
- should be set to 
-\family typewriter
 \size small
-1
+on
 \family default
 \size default
-.
- Then the coordinate is reading from the file specified by 
+, the top surface velocity boundary conditions are read in from files which
+ have location and name specified by 
 \family typewriter
 \size small
-coor_file
-\family default
+vel_bound_file
 \size default
 .
- If 
-\family typewriter
-\size small
-coor
+
 \family default
-\size default
- is set to 
-\size small
-2
-\size default
-, then there will be uniform mesh in the latitudinal and longitudinal directions.
- The mesh in the radial direction is generated according to 
+ Requires setting 
 \family typewriter
 \size small
-coor_refine
+topvbc=1
 \family default
 \size default
-, which is a vector of 4 numbers.
- The 1st value of 
+ to take effect.
+ If you wish to have a uniform top surface velocity boundary condition or
+ some simple geometric pattern, then 
 \family typewriter
 \size small
-coor_refine
+file_vbcs
 \family default
 \size default
- specifies the radius fraction of the bottom layer, the 2nd value specifies
- the fraction of the nodes in the bottom layer, the 3rd values specifies
- the top layer fraction, and the last value specifies the top layer node
- fraction.
+ should be set to zero.
+ 
 \end_layout
 
 \end_inset
@@ -12477,7 +12362,7 @@
 \begin_layout Standard
 \noindent
 \begin_inset Tabular
-<lyxtabular version="3" rows="7" columns="2">
+<lyxtabular version="3" rows="9" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -12501,41 +12386,29 @@
 Choose the format and layout of the output files.
  Can be either 
 \family typewriter
-\size small
 ascii
 \family default
-\size default
 , 
 \family typewriter
-\size small
 ascii-gz
 \family default
-\size default
  or 
 \family typewriter
-\size small
 hdf5
 \family default
-\size default
 .
  If 
 \family typewriter
-\size small
 ascii-gz
 \family default
-\size default
  is chosen, the code places gzipped files into 
 \family typewriter
-\size small
 data_dir
 \family default
-\size default
 , and will put all time-step output into subdirectories of 
 \family typewriter
-\size small
 data_dir
 \family default
-\size default
 .
  The same naming logic holds for reading old velo files.
 \end_layout
@@ -12564,52 +12437,40 @@
 \begin_layout Standard
 Choose additional output, including 
 \family typewriter
-\size small
 surf
 \family default
-\size default
 , 
 \family typewriter
-\size small
 botm
 \family default
-\size default
 , 
 \family typewriter
-\size small
 geoid
 \family default
-\size default
 , 
 \family typewriter
-\size small
+seismic
+\family default
+, 
+\family typewriter
 stress
 \family default
-\size default
 , 
 \family typewriter
-\size small
 pressure
 \family default
-\size default
 , 
 \family typewriter
-\size small
 connectivity
 \family default
-\size default
 , 
 \family typewriter
-\size small
 horiz_avg, tracer, heating, comp_el
 \family default
-\size default
  and
 \family typewriter
-\size small
  comp_nd
 \family default
-\size default
 .
 \end_layout
 
@@ -12659,23 +12520,17 @@
 \begin_layout Standard
 Controls the prefix of output file names such as 
 \family typewriter
-\size small
 regtest.xxx
 \family default
-\size default
 .
  Cannot contain the ``
 \family typewriter
-\size small
 /
 \family default
-\size default
 '' character if 
 \family typewriter
-\size small
 output_format=ascii
 \family default
-\size default
 .
 \end_layout
 
@@ -12776,6 +12631,51 @@
 \end_inset
 </cell>
 </row>
+<row bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+self_gravitation=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Considering the effect the self gravitation on the geoid or not.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+use_cbf_topo=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Using the Consistent Boundary Flux (CBF) method to compute the dynamic topograph
+y or not.
+\end_layout
+
+\end_inset
+</cell>
+</row>
 </lyxtabular>
 
 \end_inset
@@ -12889,11 +12789,12 @@
 
 \begin_layout Standard
 These specify the number of FEM nodes in each spherical cap.
+ These parameters are not used in the C version if multigrid solver is used.
 \newline
 
 \newline
-For a full spherical
- model, 
+For
+ a full spherical model, 
 \family typewriter
 nodex
 \family default
@@ -12938,10 +12839,12 @@
 \end_inset
 
  must be satisfied.
+ These parameters are not used in the C version if conjgrad solver is used.
 \newline
 
 \newline
-For a full spherical model, 
+For
+ a full spherical model, 
 \family typewriter
 mgunitx
 \family default
@@ -12968,7 +12871,7 @@
 \begin_layout Standard
 \noindent
 \begin_inset Tabular
-<lyxtabular version="3" rows="2" columns="2">
+<lyxtabular version="3" rows="3" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -13051,8 +12954,8 @@
  are the inner and outer radii in non-dimensional units.
  It is probably more convenient to normalize lengths by the radius of the
  Earth.
- If you do this, then the Rayleigh number, given below, must be calculated
- with the radius of the Earth, not the thickness of the mantle.
+ If you do this, then the Rayleigh number must be calculated with the radius
+ of the Earth, not the thickness of the mantle.
  The core mantle boundary is close to having a non-dimensional radius of
  0.55.
 \end_layout
@@ -13060,6 +12963,77 @@
 \end_inset
 </cell>
 </row>
+<row bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+coor
+\size small
+=0
+\newline
+
+\family default
+\size default
+
+\newline
+
+\family typewriter
+coor_file="coor.dat"
+\newline
+coor_refine=0.1,0.15,0.1,0.2
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If 
+\family typewriter
+coor=0
+\family default
+, there will be uniform mesh in the latitudinal, longitudinal, and radial
+ directions.
+ 
+\newline
+If 
+\family typewriter
+coor=1
+\family default
+, the coordinate is reading from the file specified by 
+\family typewriter
+coor_file
+\family default
+.
+ This is used to have a regular but uneven spacing between elements.
+\newline
+If 
+\family typewriter
+coor=
+\family default
+2, there will be uniform mesh in the latitudinal and longitudinal directions.
+ The mesh in the radial direction is generated according to 
+\family typewriter
+coor_refine
+\family default
+, which is a vector of 4 numbers.
+ The 1st value of 
+\family typewriter
+coor_refine
+\family default
+ specifies the radius fraction of the bottom layer, the 2nd value specifies
+ the fraction of the nodes in the bottom layer, the 3rd values specifies
+ the top layer fraction, and the last value specifies the top layer node
+ fraction.
+\end_layout
+
+\end_inset
+</cell>
+</row>
 </lyxtabular>
 
 \end_inset
@@ -13215,7 +13189,7 @@
 
 \family default
 \size default
-(only in non-Pyre version)
+(only in pure C version)
 \family typewriter
 \size small
 
@@ -13272,7 +13246,7 @@
 
 \begin_layout Standard
 Controls the termination of the code based on total wall clock time used.
- Available only in non-Pyre version.
+ Available only in pure C version.
 \end_layout
 
 \end_inset
@@ -13899,7 +13873,7 @@
 \family typewriter
 toptbcval
 \family default
- specifies the surface heatflux (not working in this version).
+ specifies the surface heat flux (not working in this version).
  If 
 \family typewriter
 toptbc
@@ -15193,6 +15167,8 @@
 \family typewriter
 \size small
 remove_rigid_rotation=on
+\newline
+remove_angular_momentum=on
 \end_layout
 
 \end_inset
@@ -15201,7 +15177,8 @@
 \begin_inset Text
 
 \begin_layout Standard
-Whether to remove rigid body rotation component from the velocity solution.
+Whether to remove rigid body rotation component or net angular momentum
+ from the velocity solution.
  Only effective for global models.
 \end_layout
 
@@ -15256,7 +15233,7 @@
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Standard
@@ -15283,11 +15260,13 @@
 vlowstep=1000
 \newline
 vhighstep=3
+\newline
+max_mg_cycles=50
 \end_layout
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Standard
@@ -15340,11 +15319,19 @@
 vhighstep
 \family default
 \size default
- are the number of smoothing passes at lowest/highest levels; all these
- parameters should be small integers.
- For 
+ are the number of smoothing passes at lowest/highest levels; 
 \family typewriter
 \size small
+max_mg_cycles
+\family default
+\size default
+ is the maximum number of multigrid cycles used per solve; all these parameters
+ should be small integers.
+ 
+\newline
+For 
+\family typewriter
+\size small
 cgrad
 \family default
 \size default
@@ -15375,7 +15362,7 @@
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Standard
@@ -15393,9 +15380,7 @@
 
 \family typewriter
 \size small
-accuracy=1.0e-6
-\newline
-tole_compressibility=1.0e-7
+accuracy=1.0e-4
 \end_layout
 
 \end_inset
@@ -15422,8 +15407,6 @@
 uzawa=cg
 \newline
 compress_iter_maxstep=100
-\newline
-relative_err_accuracy=0.001
 \end_layout
 
 \end_inset
@@ -15451,8 +15434,7 @@
 cg
 \family default
 \size default
-, additional parameters control the maximum iterations and desired accuracy
- for the solver.
+, additional parameters control the maximum iterations.
 \end_layout
 
 \end_inset
@@ -16121,7 +16103,7 @@
  to 
 \family typewriter
 \size small
-restart=on
+tic_method=-1
 \family default
 \size default
 .
@@ -16470,8 +16452,6 @@
 Problem=convection
 \newline
 Geometry=sphere
-\newline
-Spacing=regular
 \end_layout
 
 \end_inset
@@ -16709,7 +16689,7 @@
 \begin_layout Standard
 \noindent
 \begin_inset Tabular
-<lyxtabular version="3" rows="3" columns="2">
+<lyxtabular version="3" rows="4" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -16771,7 +16751,7 @@
 \end_inset
 </cell>
 </row>
-<row topline="true" bottomline="true">
+<row topline="true">
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
@@ -16784,7 +16764,7 @@
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Standard
@@ -16797,6 +16777,33 @@
 \end_inset
 </cell>
 </row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+\size small
+command
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+The command used to launch the job.
+ The default value should be customized if using any job scheduler, otherwise,
+ the default value should work well.
+\end_layout
+
+\end_inset
+</cell>
+</row>
 </lyxtabular>
 
 \end_inset
@@ -16813,6 +16820,34 @@
 
 \begin_layout Standard
 The scheduler facility controls how CitcomS submits jobs to a batch scheduler.
+ Available schedulers include: 
+\family typewriter
+none
+\family default
+ (default, not using a batch scheduler), 
+\family typewriter
+lsf
+\family default
+ (for Load Sharing Facility batch scheduler), 
+\family typewriter
+pbs
+\family default
+ (for Portable Batch System batch scheduler), 
+\family typewriter
+sge
+\family default
+ (for Sun Grid Engine batch scheduler), and tacc-ranger (a variant of PBS,
+ customized for the Ranger cluster at Texas Advanced Computing Center).
+ Only the command options for these schedulers are listed below.
+ For more information on configuring Pyre for your batch system, see CIG's
+ 
+\begin_inset LatexCommand htmlurl
+name "Pythia page"
+target "geodynamics.org/cig/software/packages/cs/pythia/docs/batch"
+
+\end_inset
+
+.
 \end_layout
 
 \begin_layout Standard
@@ -17145,7 +17180,7 @@
 
 \begin_layout Standard
 \begin_inset Tabular
-<lyxtabular version="3" rows="22" columns="2">
+<lyxtabular version="3" rows="23" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -17387,6 +17422,29 @@
 
 \family typewriter
 \size small
+tracer 
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+A facility for tracer parameters.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+\size small
 visc
 \end_layout
 
@@ -17695,7 +17753,7 @@
 \begin_layout Standard
 \noindent
 \begin_inset Tabular
-<lyxtabular version="3" rows="17" columns="2">
+<lyxtabular version="3" rows="16" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -17707,30 +17765,6 @@
 
 \family typewriter
 \size small
-nproc_surf=1 or 12
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-This parameter is set by the solver facility.
- Users do not need to change it.
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-
-\family typewriter
-\size small
 nprocx=1
 \end_layout
 
@@ -18394,7 +18428,7 @@
 
 \family typewriter
 \size small
-accuracy=1e-06
+accuracy=1.0e-4
 \end_layout
 
 \end_inset
@@ -18417,7 +18451,7 @@
 
 \family typewriter
 \size small
-tole_compressibility=1e-07
+uzawa=cg
 \end_layout
 
 \end_inset
@@ -18440,7 +18474,7 @@
 
 \family typewriter
 \size small
-uzawa=cg
+compress_iter_maxstep=100
 \end_layout
 
 \end_inset
@@ -18463,7 +18497,7 @@
 
 \family typewriter
 \size small
-compress_iter_maxstep=100
+mg_cycle=1 
 \end_layout
 
 \end_inset
@@ -18486,7 +18520,7 @@
 
 \family typewriter
 \size small
-relative_err_accuracy=0.001
+down_heavy=3
 \end_layout
 
 \end_inset
@@ -18509,7 +18543,7 @@
 
 \family typewriter
 \size small
-mg_cycle=1 
+up_heavy=3
 \end_layout
 
 \end_inset
@@ -18532,7 +18566,7 @@
 
 \family typewriter
 \size small
-down_heavy=3
+vlowstep=1000
 \end_layout
 
 \end_inset
@@ -18555,7 +18589,7 @@
 
 \family typewriter
 \size small
-up_heavy=3
+vhighstep=3
 \end_layout
 
 \end_inset
@@ -18578,7 +18612,7 @@
 
 \family typewriter
 \size small
-vlowstep=1000
+max_mg_cycles=50
 \end_layout
 
 \end_inset
@@ -18601,7 +18635,7 @@
 
 \family typewriter
 \size small
-vhighstep=3
+piterations=1000
 \end_layout
 
 \end_inset
@@ -18624,7 +18658,7 @@
 
 \family typewriter
 \size small
-piterations=1000
+aug_lagr=on
 \end_layout
 
 \end_inset
@@ -18647,7 +18681,7 @@
 
 \family typewriter
 \size small
-aug_lagr=on
+aug_number=2000
 \end_layout
 
 \end_inset
@@ -18662,7 +18696,7 @@
 \end_inset
 </cell>
 </row>
-<row topline="true">
+<row topline="true" bottomline="true">
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
@@ -18670,7 +18704,7 @@
 
 \family typewriter
 \size small
-aug_number=2000
+remove_rigid_rotation=on
 \end_layout
 
 \end_inset
@@ -18685,7 +18719,7 @@
 \end_inset
 </cell>
 </row>
-<row topline="true" bottomline="true">
+<row bottomline="true">
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
@@ -18693,7 +18727,7 @@
 
 \family typewriter
 \size small
-remove_rigid_rotation=on
+remove_angular_momentum=on
 \end_layout
 
 \end_inset
@@ -19411,7 +19445,7 @@
 \begin_layout Standard
 \noindent
 \begin_inset Tabular
-<lyxtabular version="3" rows="14" columns="2">
+<lyxtabular version="3" rows="15" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -19676,6 +19710,29 @@
 
 \family typewriter
 \size small
+mantle_temp=1.0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+\size small
 blob_center=[-999,-999,-999] 
 \end_layout
 
@@ -19753,7 +19810,7 @@
 
 \begin_layout Standard
 \begin_inset Tabular
-<lyxtabular version="3" rows="11" columns="2">
+<lyxtabular version="3" rows="13" columns="2">
 <features>
 <column alignment="left" valignment="top" leftline="true" width="1.85in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -19835,6 +19892,50 @@
 \begin_layout Standard
 
 \family typewriter
+self_gravitation=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+use_cbf_topo=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
 \size small
 cb_block_size=1048576
 \end_layout
@@ -20093,12 +20194,12 @@
 
 \family typewriter
 \size small
-file_vbcs=off
+mineral_physics_model=3
 \end_layout
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Standard
@@ -20116,7 +20217,7 @@
 
 \family typewriter
 \size small
-vel_bound_file="bvel.dat"
+file_vbcs=off
 \end_layout
 
 \end_inset
@@ -20139,7 +20240,7 @@
 
 \family typewriter
 \size small
-mat_control=off
+vel_bound_file="bvel.dat"
 \end_layout
 
 \end_inset
@@ -20162,7 +20263,7 @@
 
 \family typewriter
 \size small
-mat_file="mat.dat"
+mat_control=off
 \end_layout
 
 \end_inset
@@ -20185,7 +20286,7 @@
 
 \family typewriter
 \size small
-lith_age=off
+mat_file="mat.dat"
 \end_layout
 
 \end_inset
@@ -20208,7 +20309,7 @@
 
 \family typewriter
 \size small
-lith_age_file="age.dat"
+lith_age=off
 \end_layout
 
 \end_inset
@@ -20231,7 +20332,7 @@
 
 \family typewriter
 \size small
-lith_age_time=off
+lith_age_file="age.dat"
 \end_layout
 
 \end_inset
@@ -20254,7 +20355,7 @@
 
 \family typewriter
 \size small
-lith_age_depth=0.0314
+lith_age_time=off
 \end_layout
 
 \end_inset
@@ -20277,7 +20378,7 @@
 
 \family typewriter
 \size small
-mantle_temp=1.0
+lith_age_depth=0.0314
 \end_layout
 
 \end_inset
@@ -23010,7 +23111,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-colatitude longitude topography heatflux vel_colat vel_lon 
+colatitude longitude topography heat_flux vel_colat vel_lon 
 \end_layout
 
 \begin_layout Section
@@ -23154,7 +23255,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-topography heatflux vel_colat vel_lon
+topography heat_flux vel_colat vel_lon
 \end_layout
 
 \begin_layout Subsection



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