[cig-commits] r4968 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Oct 13 00:39:03 PDT 2006
Author: tan2
Date: 2006-10-13 00:39:03 -0700 (Fri, 13 Oct 2006)
New Revision: 4968
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
* Fixed a typo "PHDF HOME" -> "PHDF_HOME"
* Added a section on using none-pyre version
* Undid a xref in section 3.1, which should link to (not-checked-in-yet)
"Working with HDF5" chapter
* Updated Appendix A and changed the title
* Added description on new output files (stress, pressure, average)
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-13 06:43:36 UTC (rev 4967)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-13 07:39:03 UTC (rev 4968)
@@ -2012,7 +2012,7 @@
By default, CitcomS will attempt to auto-detect your PHDF5 installation,
and will disable HDF5 support if it is not found.
You may explicitly specify the location of your PHDF5 installation by setting
- the PHDF5 HOME environment variable to the appropriate installation prefix.
+ the PHDF5_HOME environment variable to the appropriate installation prefix.
\end_layout
\begin_layout LyX-Code
@@ -2603,23 +2603,80 @@
\end_layout
\begin_layout Section
-Using CitComS.py
+Using CitComS.py Without Pyre
\end_layout
\begin_layout Standard
-CitComS.py usage is similar to that of previous versions of CitComS.
- Installed under the
+Whether you build CitComS.py with or without Pyre framework, two binary executabl
+es
\family typewriter
+CitcomSRegional
+\family default
+ and
+\family typewriter
+CitcomSFull
+\family default
+ are installed under the
+\family typewriter
bin
\family default
directory (default
\family typewriter
/usr/local/bin
\family default
-), the program
+).
+ These programs do not use the Pyre framework.
+ Their usage is the same:
+\end_layout
+
+\begin_layout LyX-Code
+$ mpirun [mpi_options] CitcomSRegional inputfile
+\newline
+$ mpirun [mpi_options] CitcomSFu
+ll inputfile
+\end_layout
+
+\begin_layout Standard
+Two inputfile examples, one for regional spherical model and one for full
+ spherical model, are provided in the
\family typewriter
+examples/Regional
+\family default
+ and
+\family typewriter
+examples/Full
+\family default
+ directories, respectively.
+ The meaning of the input parameters is described in Appendix
+\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Section
+Using CitComS.py with Pyre
+\end_layout
+
+\begin_layout Standard
+If you build CitComS.py with Pyre framework, a program
+\family typewriter
citcoms
\family default
+ is installed under the
+\family typewriter
+bin
+\family default
+ directory (default
+\family typewriter
+/usr/local/bin
+\family default
+).
+ The program
+\family typewriter
+citcoms
+\family default
is used for running both the regional and full spherical models.
The program
\family typewriter
@@ -2638,7 +2695,7 @@
\begin_layout Standard
On input, CitComS.py needs numerous parameters specified (see Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-A:-Facilities,}
+\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
\end_inset
@@ -2650,13 +2707,12 @@
as the Rayleigh number).
These input parameters, or properties in the Pyre terminology, are grouped
under several Pyre components.
- You can think
\end_layout
\begin_layout Standard
Most of the properties you will set using CitComS.py have identical names
as the parameters for the old CitComS, which is described in Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-A:-Facilities,}
+\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
\end_inset
@@ -3288,9 +3344,9 @@
a single HDF5 (Hierarchical Data Format) file.
The HDF5 file takes less disk space than the ASCII files in total and doesn't
require additional post-processing to be visualized in OpenDX.
- In order to use this feature, you need to compile CitComS.py with the parallel
- HDF5 library (see
-\begin_inset LatexCommand \ref{sec:HDF5-Configuration}
+ In order to use this feature, you need to compile CitComS.py with parallel
+ HDF5 library (see Section
+\begin_inset LatexCommand \vref{sec:HDF5-Configuration}
\end_inset
@@ -3316,13 +3372,8 @@
/home/username/example1.h5
\family default
.
- See section\InsetSpace ~
-
-\begin_inset LatexCommand \ref{sec:HDF5-Configuration}
-
-\end_inset
-
- for more information on how to work with HDF5 output.
+ See Chapter (TODO: link to hdf5 chapter) for more information on how to
+ work with HDF5 output.
\end_layout
\begin_layout Subsection
@@ -5718,39 +5769,30 @@
\begin_layout Chapter
\start_of_appendix
-\begin_inset LatexCommand \label{cha:Appendix-A:-Facilities,}
+\begin_inset LatexCommand \label{cha:Appendix-A:-Input}
\end_inset
-Facilities, Properties, and Parameters
+Input Parameters for CitComS.py
\end_layout
\begin_layout Section
-Introduction
+Input Parameters Grouped by Functionality
\end_layout
\begin_layout Standard
-Most of the properties have identical names for the parameters as those
- used in the none-pyre version of CitComS.
- This section highlights those which have changed and those which are entirely
- new.
- All the parameters which can be set are included in an appendix at the
- end of this documentation.
+This section explains the meaning the input parameters for CitComS.py.
+ These parameters are grouped by their functionality.
Parameters are given with their default values.
-
\end_layout
-\begin_layout Section
-Input parameters
-\end_layout
-
\begin_layout Subsection
Parameters that Control Input Files
\end_layout
\begin_layout Standard
\begin_inset Tabular
-<lyxtabular version="3" rows="9" columns="2">
+<lyxtabular version="3" rows="5" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -5759,7 +5801,17 @@
\begin_inset Text
\begin_layout Standard
-datadir="."
+file_vbcs=off
+\newline
+vel_bound_file=
+\begin_inset Quotes srd
+\end_inset
+
+bvel.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -5768,11 +5820,27 @@
\begin_inset Text
\begin_layout Standard
+If
+\family typewriter
+file_vbcs
+\family default
+ is set to on, the top surface velocity boundary conditions are read in
+ from files which have location and name specified by
+\family typewriter
+vel_bound_file.
+\family default
+ Requires setting
\family typewriter
-datadir
+topvbc=1
\family default
- controls the location of output files.
+ to take effect.
+ If you wish to have a uniform top surface velocity boundary condition or
+ some simple geometric pattern, then
+\family typewriter
+file_vbcs
+\family default
+ should be set to zero.
\end_layout
@@ -5784,7 +5852,17 @@
\begin_inset Text
\begin_layout Standard
-datafile="regtest"
+coor=off
+\newline
+coor_file=
+\begin_inset Quotes srd
+\end_inset
+
+coor.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -5793,32 +5871,87 @@
\begin_inset Text
\begin_layout Standard
-
+If
\family typewriter
-datafile
+coor
\family default
- controls the prefix of output filenames.
- Files such as regtest.xxx.
- The prefix cannot contain the
-\begin_inset Quotes sld
+ is set to off, 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,
+\family typewriter
+coor
+\family default
+ should be set to on.
+ Then, the coordinate is reading from the file specified by
+\family typewriter
+coor_file
+\family default
+.
+\end_layout
+
\end_inset
+</cell>
+</row>
+<row topline="true" newpage="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
-/
+\begin_layout Standard
+mat_control=off
+\newline
+mat_file=
\begin_inset Quotes srd
\end_inset
- character.
+mat.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If
+\family typewriter
+mat_control
+\family default
+ is set to on, then the time- and positional- dependent viscosity factor
+ is defined from the files specified by
+\family typewriter
+mat_file
+\family default
+.
+ These parameters allow you to define the material group of each element
+ (such as a moving weak zone).
+ Not working in this version.
+\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
-file_vbcs=0
+lith_age=off
+\newline
+lith_age_file=
+\begin_inset Quotes srd
+\end_inset
+
+age.dat
+\begin_inset Quotes srd
+\end_inset
+
+
+\newline
+lith_age_time=off
\end_layout
\end_inset
@@ -5829,33 +5962,33 @@
\begin_layout Standard
If
\family typewriter
-file_vbcs
+lith_age
\family default
- is true (it is set=1) then the top surface velocity boundary conditions
- are read in from files which have location and name specified by
+ is set to on, then the age of each surface nodes is read from the files
+ specified by
\family typewriter
-vel_bound_file.
-
+lith_age_file
\family default
- The conditions on the top surface must be correctly set, as indicated below.
- If you wish to have a uniform top surface velocity boundary condition or
- some simple geometric pattern, then
+.
+ These parameters control the thermal age of the top thermal boundary condition.
+ If
\family typewriter
-file_vbcs
+lith_age_time
\family default
- should be set to zero.
-
+ is on, the files are time-dependent.
\end_layout
\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
\begin_layout Standard
-vel_bound_file=""
+tracer=off
+\newline
+tracer_file=tracer.dat
\end_layout
\end_inset
@@ -5864,27 +5997,47 @@
\begin_inset Text
\begin_layout Standard
-See explanation for
-\family typewriter
-file_vbcs
-\family default
-, above.
- Velocity boundary conditions are read by setting the pathway to the boundary
- conditions file, e.g.,
-\family typewriter
-\size footnotesize
-vel_bound_file="/username/Models/New_Tonga/Vel/bvel.dat"
+This controls the tracer particles which are advected passively by the flow.
+ This part of the code has not been made parallel and must be used with
+ caution with the present implementation.
+
\end_layout
\end_inset
</cell>
</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Parameters that Control Output Files
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-coor=off
+output_format=
+\begin_inset Quotes srd
+\end_inset
+
+ascii-local
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -5893,21 +6046,32 @@
\begin_inset Text
\begin_layout Standard
-If you wish to have a regular, but uneven, spacing between elements then
-
-\family typewriter
-coor
-\family default
- should be set to on.
- If
-\family typewriter
-coor
-\family default
- is set to off, then there will be uniform mesh in the latitudinal, longitudinal
-, and radial directions, e.g.,
-\family typewriter
-\size small
-coor_file="/username/Models/New_Tonga/Case2/coor.dat"
+Choose the format and layout of the output files.
+ Can either
+\begin_inset Quotes sld
+\end_inset
+
+ascii-local
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+ascii
+\begin_inset Quotes srd
+\end_inset
+
+, or
+\begin_inset Quotes sld
+\end_inset
+
+hdf5
+\begin_inset Quotes srd
+\end_inset
+
+.
\end_layout
\end_inset
@@ -5918,34 +6082,83 @@
\begin_inset Text
\begin_layout Standard
-coor_file=""
+output_optional=
+\begin_inset Quotes srd
+\end_inset
+
+surf,botm
+\begin_inset Quotes srd
+\end_inset
+
+
\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
-See
-\family typewriter
-coor
-\family default
-, above, e.g.,
-\family typewriter
-\size small
-coor_file="/username/Models/New_Tonga/Case2/coor.dat"
+Choose additional output, including:
+\begin_inset Quotes sld
+\end_inset
+
+surf
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+botm
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+stress
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+pressure
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+connectivity
+\begin_inset Quotes srd
+\end_inset
+
+, and
+\begin_inset Quotes sld
+\end_inset
+
+horiz_avg
+\begin_inset Quotes srd
+\end_inset
+
+.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" newpage="true">
+<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-mat_control=0
+datadir="."
\end_layout
\end_inset
@@ -5954,18 +6167,12 @@
\begin_inset Text
\begin_layout Standard
-
+Controls the location of output files.
+ Only significant if
\family typewriter
-\size small
-mat_file="/home/clint/back/ra8/mat.dat"
+output_format=ascii
\family default
-\size default
- If mat_control is true (it is set=1) then the time- and positional-dependent
- viscosity factor is defined by file having location and name specified
- bymat_file.
- These parameters allow you to define the material group of each element
- (such as a moving weak zone).
-
+.
\end_layout
\end_inset
@@ -5976,7 +6183,11 @@
\begin_inset Text
\begin_layout Standard
-lith_age=0
+datafile="regtest
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -5985,15 +6196,21 @@
\begin_inset Text
\begin_layout Standard
+Controls the prefix of output filenames.
+ Files such as regtest.xxx.
+ Cannot contain the
+\begin_inset Quotes sld
+\end_inset
+/
+\begin_inset Quotes srd
+\end_inset
+
+ character if
\family typewriter
-\size footnotesize
-lith_age_file="/username/Models/New_Tonga/Case6/age.dat"
+output_format=ascii
\family default
-\size default
- If lith_age is true (it is set=1) then the lith_age_file is read.
- These parameters control the thermal age of the top thermal boundary condition.
-
+.
\end_layout
\end_inset
@@ -6004,7 +6221,16 @@
\begin_inset Text
\begin_layout Standard
-tracer=0
+storage_spacing=10
+\newline
+(in none-pyre version)
+\newline
+or
+\newline
+monitoringFrequency=10
+\newline
+(in pyre
+ version)
\end_layout
\end_inset
@@ -6013,16 +6239,12 @@
\begin_inset Text
\begin_layout Standard
-
-\family typewriter
-\size small
-tracer_file=""
-\family default
-\size default
- This controls the tracer particles which are advected passively by the
- flow.
- This part of the code has not been made parallel and must be used with
- caution with the present implementation.
+Controls the interval between output files.
+ CitComS.py dynamically determines the size of the time step; this means
+ that you might not get an output at the exact time required, but you can
+ always get close depending on how small this number is.
+ Do not make this number too small since outputs slow the code down and
+ you may end up with an unmanageable number of output files.
\end_layout
@@ -6037,18 +6259,13 @@
\end_layout
\begin_layout Subsection
-Mesh Set-up and Processors
+Mesh and Processors Setup
\end_layout
\begin_layout Standard
-Parameters control the logical set-up of the mesh as well as the number
- of processors in the three coordinate directions.
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="2">
+<lyxtabular version="3" rows="4" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -6066,9 +6283,8 @@
\begin_inset Text
\begin_layout Standard
-This specifies the number of spherical caps of the mesh, must be 1 for CitComS.py
- and 12 for fullCitComS.
-
+This specifies the number of spherical caps of the mesh, must be 1 for regional
+ spherical model and 12 for full spherical model.
\end_layout
\end_inset
@@ -6079,9 +6295,9 @@
\begin_inset Text
\begin_layout Standard
-nprocx=2
+nprocx=1
\newline
-nprocy=2
+nprocy=1
\newline
nprocz=1
\end_layout
@@ -6093,6 +6309,17 @@
\begin_layout Standard
These specify the number of processors in each spherical cap.
+
+\newline
+
+\newline
+For full spherical model,
+\family typewriter
+nprocx
+\family default
+ must equal to
+\family typewriter
+nprocy
\end_layout
\end_inset
@@ -6103,9 +6330,9 @@
\begin_inset Text
\begin_layout Standard
-nodex=17
+nodex=9
\newline
-nodey=17
+nodey=9
\newline
nodez=9
\end_layout
@@ -6117,13 +6344,23 @@
\begin_layout Standard
These specify the number of FEM nodes in each spherical cap.
-
+\newline
+
+\newline
+For full spherical
+ model,
+\family typewriter
+nodex
+\family default
+ must equal to
+\family typewriter
+nodey
\end_layout
\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
@@ -6146,45 +6383,34 @@
These specify the nested level of multigrid unit.
Used by multigrid solver only.
These parameters are not completely independent to each other.
- Some constraints must be satisfied:
+ Following constraints must be satisfied:
\newline
\newline
-nodex = 1 + nprocx * mgunitx * 2 **
- (levels-1)
+
+\family typewriter
+nodex = 1 + nprocx * mgunitx * 2**(levels-1)
\newline
-nodey = 1 + nprocy * mgunity * 2 ** (levels-1)
+nodey = 1 + nprocy * mgunity
+ * 2**(levels-1)
\newline
-nodez = 1 + nprocz
- * mgunitz * 2 ** (levels-1)
-\end_layout
+nodez = 1 + nprocz * mgunitz * 2**(levels-1)
+\family default
-\end_inset
-</cell>
-</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
+\newline
-\begin_layout Standard
-nprocx=nprocy;
\newline
-nodex=nodey;
-\newline
-mgunitx=mgunity
+For full spherical model,
+\family typewriter
+mgunitx
+\family default
+ must equal to
+\family typewriter
+mgunity
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-For fullCitComS only
-\end_layout
-
-\end_inset
-</cell>
</row>
</lyxtabular>
@@ -6200,12 +6426,6 @@
\begin_layout Standard
\noindent
-Parameters which control the actual physical size of the domain (a cut out
- of a sphere).
-\end_layout
-
-\begin_layout Standard
-\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features islongtable="true">
@@ -6216,7 +6436,7 @@
\begin_inset Text
\begin_layout Standard
-theta_min=1.0780
+theta_min=1.0708
\newline
theta_max=2.0708
\newline
@@ -6231,11 +6451,26 @@
\begin_inset Text
\begin_layout Standard
-theta_min and theta_max are the colatitude measured in radians from the
- north pole.
- fi_min and fi_max are the longitudes measured from the prime meridian eastward
- in radians.
- Only in CitComS.py.
+These parameters specify the horizontal extent of the computation domain.
+
+\family typewriter
+theta_min
+\family default
+ and
+\family typewriter
+theta_max
+\family default
+ are the colatitude measured in radians from the north pole.
+
+\family typewriter
+fi_min
+\family default
+ and
+\family typewriter
+fi_max
+\family default
+ are the longitudes measured from the prime meridian eastward in radians.
+ Only in regional CitComS.py.
\end_layout
\end_inset
@@ -6257,8 +6492,16 @@
\begin_inset Text
\begin_layout Standard
-radius_inner and radius_outer are the inner and outer radius in non-dimensional
- units.
+These parameters specify the radial extent of the computation domain.
+
+\family typewriter
+radius_inner
+\family default
+ and
+\family typewriter
+radius_outer
+\family default
+ are the inner and outer radius in non-dimensional units.
It is probably most convenient to normalize lengths by the radius of the
Earth.
If you do this, then the Rayleigh number, given below, must be calculated
@@ -6282,13 +6525,9 @@
\end_layout
\begin_layout Standard
-Parameters which control the restarting of the code.
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="2" columns="2">
+<lyxtabular version="3" rows="4" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -6297,34 +6536,96 @@
\begin_inset Text
\begin_layout Standard
-restart=0
+restart=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If
+\family typewriter
+restart
+\family default
+ is on, eacho processor will read its initial temperature field from a velo
+ file.
+\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
+post_p=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Similar to
+\family typewriter
+restart
+\family default
+, except that the model will then only run for 1 time step, which can be
+ useful to regenerate the flow field and calculate the associated observables.
+\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
+datadir_old=
+\begin_inset Quotes srd
+\end_inset
+
+.
+\begin_inset Quotes srd
+\end_inset
+
+
\newline
-post_p=0
+datafile_old="regtest"
\newline
-datafile_old=""
-\newline
-solution_cycles_init=100
+solution_cycles_init=0
\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 restart is true, for example, processor #5 will read its initial temperature
- field formfile
+If
\family typewriter
-/scratch/test.velo.5.100
+restart
\family default
+ is on, for example, processor #5 will read its initial temperature field
+ form file
+\family typewriter
+regtest.velo.5.0
+\family default
in this case.
- If post_p is true, e.g., processor #5 will read its initial temperature field
- form file
+
\family typewriter
- /scratch/test.velo.5.100
+datadir_old
\family default
- in this case, just like when restart is true.
- But the program will run for 1 time step only.
+ is significant only if
+\family typewriter
+output_format=ascii
+\family default
+.
\end_layout
\end_inset
@@ -6335,7 +6636,7 @@
\begin_inset Text
\begin_layout Standard
-zero_elapsed_time=1
+zero_elapsed_time=on
\end_layout
\end_inset
@@ -6344,9 +6645,16 @@
\begin_inset Text
\begin_layout Standard
-If zero_elapsed_time is true, the initial time is set to zero.
- If it is false and restart or post_p is true, the initial time is read
- in from previous output files.
+If
+\family typewriter
+zero_elapsed_time
+\family default
+ is on, the initial time is set to zero.
+ If it is off and
+\family typewriter
+restart
+\family default
+ is on, the initial time is read in from previous output files.
\end_layout
\end_inset
@@ -6360,38 +6668,58 @@
\end_layout
\begin_layout Subsection
-Run Length, Output Interval
+Run Length
\end_layout
\begin_layout Standard
-Parameters which control the length of the run and the interval between
- writing output files.
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="1" columns="2">
+<lyxtabular version="3" rows="2" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
-<row topline="true" bottomline="true">
+<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
minstep=1
\newline
-run=8001
+maxtotstep=1000000
\newline
-maxtotstep=8001
+(only in none-pyre version)
\newline
-monitoringFrequency=10
+or
\newline
+steps=1
+\newline
+(only in
+ pyre version)
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+The maximum and minimum number of time steps for the model, including the
+ 0th time step.
+\end_layout
+
+\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
cpu_limits_in_seconds=
- \InsetSpace ~
+\newline
\InsetSpace ~
\InsetSpace ~
+\InsetSpace ~
360000000
\end_layout
@@ -6401,22 +6729,8 @@
\begin_inset Text
\begin_layout Standard
-The maximum number of time steps is set with run and maxtotstep.
- It is recommended that these be set to the same value.
- Add one to the total number of steps; in this example, the total steps
- is 8000.
- The minimum number of time steps is set with minstep; monitoringFrequency
- controls the interval between output files.
- CitComS dynamically determines the non-dimensional time step (such as _t);
- this means that you might not get an output at the exact time required,
- but you can always get close depending on how small monitoringFrequency
- is.
- Do not make this number too small since outputs slow the code down and
- you may end up with an unmanageable number of output files.
- You can also control the termination of the code based on total wall clock
- time using cpu_limits_in_seconds.
- If you are just learning to use the code, you might want to give this a
- small value so that it doesn't burn up valuable computer time.
+Control the termination of the code based on total wall clock time used.
+ Available only in none-pyre version.
\end_layout
\end_inset
@@ -6436,7 +6750,7 @@
\begin_layout Standard
\align center
\begin_inset Tabular
-<lyxtabular version="3" rows="1" columns="2">
+<lyxtabular version="3" rows="3" columns="2">
<features>
<column alignment="center" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -6446,41 +6760,148 @@
\begin_layout Standard
\align left
+tic_method=0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Which method to use to generate the initial temperature field.
+\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
+\align left
num_perturbations=1
\newline
perturbmag=0.05
\newline
-perturbl=1
+perturbl=1
\newline
-perturbm=1
+perturbm=1
\newline
perturblayer=5
\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
-The initial temperature is a linear temperature gradient with some perturbations
-, and num_perturbations specifies the number of perturbations.
+Used only if
+\family typewriter
+tic_method
+\family default
+=0.
+ The initial temperature is a linear temperature gradient with some perturbation
+s, and
+\family typewriter
+num_perturbations
+\family default
+ specifies the number of perturbations.
The amplitude of the perturbations is specified in the list of real numbers
- by perturbmag.
- In fullCitComS, perturbl and perturbm specify the shape of the perturbations
- in spherical harmonic degree and order; perturblayer specifies the layers
- to be perturbed.
- In regitcoms, perturbl and preturbm specify the number of nodal lines in
- longitudinal and latitudinal directions; perturblayer is not used, although
- the pertublayer represents the number of the mesh node in radiad direction.
- There must be as many entries in a comma-separated list as in num_perturbations.
- No spaces are allowed in the list.
+ by
+\family typewriter
+perturbmag
+\family default
+.
+ In full spherical model,
+\family typewriter
+perturbl
+\family default
+ and
+\family typewriter
+perturbm
+\family default
+ specify the shape of the perturbations in spherical harmonic degree and
+ order.
+ In region model,
+\family typewriter
+perturbl
+\family default
+ and
+\family typewriter
+preturbm
+\family default
+ specify the number of nodal lines in longitudinal and latitudinal directions.
+\family typewriter
+perturblayer
+\family default
+ specifies the layers to be perturbed, representing the number of the mesh
+ node in radial direction.
+ There must be as many entries as
+\family typewriter
+num_perturbations
+\family default
+ in a comma-separated list .
+
\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
+half_space_age=40
+\newline
+mantle_temp=1.0
+\newline
+blob_center
+\newline
+blob_radius=0.063
+\newline
+blob_dT=0.18
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Used only if
+\family typewriter
+tic_method
+\family default
+=2 and in the regional model.
+ This create a top thermal boundary with a half-space cooling age specified
+ by
+\family typewriter
+half_space_age
+\family default
+ in million years and a warm spherical blob
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+.
+ These parameters specify the temperature of the ambient mantle, the location
+ and radius of the blob, and also the amplitude of temperature change in
+ the blob relative to the ambient mantle temperautre.
+ The location of the blob is default to the center of the computation domain.
+\end_layout
+
+\end_inset
+</cell>
+</row>
</lyxtabular>
\end_inset
@@ -6494,7 +6915,7 @@
\begin_layout Standard
\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="2">
+<lyxtabular version="3" rows="7" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -6517,10 +6938,32 @@
\begin_layout Standard
Surface velocity boundary condition parameters.
- If topvbc is 0, the topvbxval and topvbyval specify the tangential surface
- stress (forced BC).
- If topvbc is 1, topvbxval and topvbyval specify the tangential surface
- velocity (fixed BC).
+ If
+\family typewriter
+topvbc
+\family default
+ is 0,
+\family typewriter
+topvbxval
+\family default
+ and
+\family typewriter
+topvbyval
+\family default
+ specify the tangential surface stress (forced BC).
+ If
+\family typewriter
+topvbc
+\family default
+ is 1,
+\family typewriter
+topvbxval
+\family default
+ and
+\family typewriter
+topvbyval
+\family default
+ specify the tangential surface velocity (fixed BC).
The surface normal velocity is zero in these two cases (impermeable BC).
If topvbc is 2, the surface normal and tangential stress are zero (permeable
BC).
@@ -6558,6 +7001,46 @@
\begin_inset Text
\begin_layout Standard
+side_sbcs=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Enable traction boundary condition for the sidewalls or not.
+\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
+pseudo_free_surf=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Enable pseudo free surface or not.
+\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
toptbc=1
\newline
toptbcval=0.0
@@ -6570,8 +7053,24 @@
\begin_layout Standard
Surface temperature boundary conditions.
- If toptbc is 0, the toptbcval specifies the surface heatflux.
- If toptbc is 1, the toptbcval specifies the surface temperature.
+ If
+\family typewriter
+toptbc
+\family default
+ is 0,
+\family typewriter
+toptbcval
+\family default
+ specifies the surface heatflux (not working in this version).
+ If
+\family typewriter
+toptbc
+\family default
+ is 1, the
+\family typewriter
+toptbcval
+\family default
+ specifies the surface temperature.
\end_layout
@@ -6606,8 +7105,14 @@
\begin_inset Text
\begin_layout Standard
-lith_age_time=0 lith_age_depth=0.031400 mantle_temp=1.000000 temperature_bound_
-adj=0 depth_bound_adj=0.157000 width_bound_adj=0.087270
+temperature_bound_adj=off
+\newline
+depth_bound_adj=0.157
+\newline
+width_bound_adj=0.08727
+\newline
+lith_age_dept
+h=0.0314
\end_layout
\end_inset
@@ -6616,7 +7121,11 @@
\begin_inset Text
\begin_layout Standard
-Boundary condition when lith_age is true.
+Additional parameters for temperature boundary condition when
+\family typewriter
+lith_age
+\family default
+ is on.
\end_layout
\end_inset
@@ -6630,14 +7139,10 @@
\end_layout
\begin_layout Subsection
-Miscellaneous
+Non-dimensional Numbers
\end_layout
\begin_layout Standard
-The following are some miscellaneous parameters.
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
@@ -6649,7 +7154,7 @@
\begin_inset Text
\begin_layout Standard
-stokes_flow_only=0 inputdiffusivity= 0.001000
+rayleigh=1.0e+5
\end_layout
\end_inset
@@ -6658,14 +7163,8 @@
\begin_inset Text
\begin_layout Standard
-stokes_flow_only is a parameter which can lead to confusion.
- If you wish only to solve for the velocity once (e.g., Stokes flow) then
- make this parameter true (i.e.
- ,1 or on).
- However, if you want to do a convection problem then this should be false,
- as indicated in the example.
- At this point, don't change the parameter inputdiffusivity -- this may
- play a role in problems which are integrated backward in time.
+This specifies the Rayleigh number, which is one of the most important parameter
+s you may want to change.
\end_layout
\end_inset
@@ -6676,7 +7175,7 @@
\begin_inset Text
\begin_layout Standard
-rayleigh=1.357e+08
+Q0=0.0
\end_layout
\end_inset
@@ -6685,9 +7184,7 @@
\begin_inset Text
\begin_layout Standard
-This specifies the Rayleigh number, which is one of the most important parameter
-s you may want to change.
- It is defined as Q0=0.0 This specifies the internal heating number.
+This specifies the internal heating number.
\end_layout
@@ -6702,7 +7199,7 @@
\end_layout
\begin_layout Subsection
-Required Information
+Depth Information
\end_layout
\begin_layout Standard
@@ -6716,15 +7213,13 @@
\begin_inset Text
\begin_layout Standard
-Problem=convection
+z_lith=0.014
\newline
-Geometry=sphere
+z_410=0.06435
\newline
-Spacing=regular
+z_lmantle=0.105
\newline
-Solver=cgrad
-\newline
-node_assemble=1
+z_cmb=0.439
\end_layout
\end_inset
@@ -6733,10 +7228,16 @@
\begin_inset Text
\begin_layout Standard
-For the version of CitComS you received in your distribution, all of these
- parameters must be set as indicated.
- You need other versions of CitComS if you wish these parameters to take
- on different geometries, problems, or mesh spacing, or use different solvers.
+Specify the non-dimensional depth of the Moho, 410km discontinuity, 660km
+ discontinuity and D".
+ These parameters are used to determine the depth of viscosity layers and
+ phase changes (see next two sections).
+ The names are only suggestive.
+ You are free to refer
+\family typewriter
+z_lith
+\family default
+ to an arbitrary depth, for example.
\end_layout
\end_inset
@@ -6750,27 +7251,22 @@
\end_layout
\begin_layout Subsection
-Depth Information
+Viscosity
\end_layout
\begin_layout Standard
+\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="1" columns="2">
+<lyxtabular version="3" rows="12" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
-<row topline="true" bottomline="true">
+<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-z_lith=0.014
-\newline
-z_410=0.06435
-\newline
-z_lmantle=0.105
-\newline
-z_cmb=0.439
+Viscosity=system
\end_layout
\end_inset
@@ -6779,48 +7275,65 @@
\begin_inset Text
\begin_layout Standard
-Specify the non-dimensional depth of Moho, 410km discontinuity, 660km discontinu
-ity and D".
- These parameters are used to determine the depth of material interfaces
- and phase changes (see next two sections).
- The names are only suggestive.
- You are free to refer z_lith to an arbitrary depth, for example.
+This parameter must be set as indicated.
\end_layout
\end_inset
</cell>
</row>
-</lyxtabular>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+\begin_layout Standard
+visc_smooth_method=3
+\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 specifies which method to smooth viscosity projection for multigrid
+ solver.
+
\end_layout
-\begin_layout Subsection
-Viscosity
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+VISC_UPDATE=on
\end_layout
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
\begin_layout Standard
-Parameters which control the viscosity.
-
+If
+\family typewriter
+VISC_UPDATE
+\family default
+ is on, viscosity will be updated every time step.
+ Othwise, viscosity will be time-independent.
\end_layout
-\begin_layout Standard
-\noindent
-\begin_inset Tabular
-<lyxtabular version="3" rows="7" columns="2">
-<features islongtable="true">
-<column alignment="left" valignment="top" leftline="true" width="1.75in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+\end_inset
+</cell>
+</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-Viscosity=system
-\newline
-rheol=3
+num_mat=4
\end_layout
\end_inset
@@ -6829,14 +7342,38 @@
\begin_inset Text
\begin_layout Standard
-For the version of CitComS you received in your distribution, all of these
- parameters must be set as indicated.
- When rheol=3, temperature dependent viscosity is computed by:
+This specifies the number of material layers.
+ Material 1 is at depth between 0 and
\family typewriter
-\size footnotesize
-viscosity = visc0 * exp( viscE/(T+viscT) - viscE/(1+viscT) )
+z_lith
\family default
-\size default
+, material 2 between
+\family typewriter
+z_lith
+\family default
+ and
+\family typewriter
+z_410
+\family default
+, material 3 between
+\family typewriter
+z_410
+\family default
+ and
+\family typewriter
+z_lmantle
+\family default
+, and material 4 between
+\family typewriter
+z_lmantle
+\family default
+ and the bottom.
+ If
+\family typewriter
+mat_control
+\family default
+ is on, then a multiplicative factor is applied to the viscosity, as defined
+ below.
\end_layout
@@ -6848,7 +7385,7 @@
\begin_inset Text
\begin_layout Standard
-visc_smooth_method=3
+visc0=1,1,1,1
\end_layout
\end_inset
@@ -6857,8 +7394,12 @@
\begin_inset Text
\begin_layout Standard
-This specifies which method to smooth viscosity projection for multigrid
- solver.
+The pre-exponent factor of layered viscosity structure.
+ There must be as many entries as
+\family typewriter
+num_mat
+\family default
+ in a comma-separated list.
\end_layout
@@ -6870,7 +7411,7 @@
\begin_inset Text
\begin_layout Standard
-VISC_UPDATE=on
+TDEPV=off
\end_layout
\end_inset
@@ -6879,8 +7420,7 @@
\begin_inset Text
\begin_layout Standard
-If visc_update is true (i.e., 1 or on), viscosity is updated every time step
- by the following parameters.
+Enable temperature dependence or not.
\end_layout
\end_inset
@@ -6891,7 +7431,7 @@
\begin_inset Text
\begin_layout Standard
-num_mat=4
+rheol=3
\end_layout
\end_inset
@@ -6900,13 +7440,33 @@
\begin_inset Text
\begin_layout Standard
-This specifies the number of material layers.
- Material 1 is at depth between 0 and z_lith, material 2 is between z_lith
- and z_410, material 3 is between z_410 and z_lmantle, and material 4 is
- between z_lmantle and (radius_outer - radius_inner).
- If mat_control is true, then a multiplicative factor is applied to the
- viscosity, as defined below.
-
+When
+\family typewriter
+rheol
+\family default
+=3, temperature-dependent viscosity is computed by:
+\family typewriter
+\size footnotesize
+
+\newline
+visc = visc0 * exp( viscE/(T+viscT) - viscE/(1+viscT) )
+\family default
+\size default
+
+\newline
+
+\newline
+When
+\family typewriter
+rheol
+\family default
+=4, temperature-dependent viscosity is computed by:
+\family typewriter
+\size footnotesize
+
+\newline
+visc = visc0 * exp( (viscE + viscZ*(1-z)) / (T+viscT) - (viscE + viscZ*(1-z))
+ / (1+viscT) )
\end_layout
\end_inset
@@ -6917,10 +7477,11 @@
\begin_inset Text
\begin_layout Standard
-TDEPV=on viscE=0.1,0.1,1.0,1.0 viscT=-1.02126,-1.01853, -1.32722,-1.32722
+viscE=1,1,1,1
\newline
-visc0=1.0e2,2.e
--3, 2.e0,2.e1
+viscT=1,1,1,1
+\newline
+viscZ=1,1,1,1
\end_layout
\end_inset
@@ -6929,11 +7490,13 @@
\begin_inset Text
\begin_layout Standard
-If TDEPV is true (i.e., 1 or on), viscE, viscT, and visc0 are parameters defining
- viscosity law.
- See the equation above.
- There must be as many entries in a comma-separated list as num_mat.
- No space is allowed in the list.
+Parameters defining viscosity law.
+ See the equations above.
+ There must be as many entries as
+\family typewriter
+num_mat
+\family default
+ in a comma-separated list.
\end_layout
@@ -6945,19 +7508,78 @@
\begin_inset Text
\begin_layout Standard
-SDEPV=off sdepv_expt=1,1,1,1,1,1,1,1 sdepv_misfit=0.020
+SDEPV=off
\end_layout
\end_inset
</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Enable stress dependence (non-Newtonian) or not.
+\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
+sdepv_expt=1,1,1,1
+\newline
+sdepv_misfit=0.02
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-If SDEPV is true (i.e., 1 or on), these specify the exponent in the viscosity
- law and the criterion of convergence test.
- There must be as many entries in a comma-separated list as num_mat.
- No space is allowed in the list.
+If
+\family typewriter
+SDEPV
+\family default
+ is on, these specify the exponent in the viscosity law and the criterion
+ of convergence test.
+ There must be as many entries as
+\family typewriter
+num_mat
+\family default
+ in a comma-separated list.
+\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
+VMIN=off
+\newline
+visc_min=0.001
+\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
+VMIN
+\family default
+ is on, minimum viscosity is cut off at
+\family typewriter
+visc_min
+\family default
+.
\end_layout
@@ -6969,7 +7591,9 @@
\begin_inset Text
\begin_layout Standard
-VMIN=on visc_min=1.e-4 VMAX=on visc_max=1.e3
+VMAX=off
+\newline
+visc_max=1000
\end_layout
\end_inset
@@ -6978,8 +7602,15 @@
\begin_inset Text
\begin_layout Standard
-If VMIN is true (i.e., 1 or on), minimum viscosity is cut off at visc_min.
- VMAX and visc_max are for the maximum viscosity cutoff.
+If
+\family typewriter
+VMAX
+\family default
+ is on, maximum viscosity is cut off at
+\family typewriter
+visc_max.
+
+\family default
\end_layout
@@ -7023,9 +7654,13 @@
\begin_inset Text
\begin_layout Standard
-These specify the phase change parameters (density change, Clapeyron slope,
- ambient temperature, and phase change width, respectively).
- The depth of this phase change is specified by z_410.
+These specify the phase change parameters (phase change Rayleigh number,
+ Clapeyron slope, ambient temperature, and phase change width, respectively).
+ The depth of this phase change is specified by
+\family typewriter
+z_410
+\family default
+.
\end_layout
\end_inset
@@ -7052,7 +7687,11 @@
\begin_layout Standard
As above.
- The depth of this phase change is specified by z_lmantle.
+ The depth of this phase change is specified by
+\family typewriter
+z_lmantle
+\family default
+.
\end_layout
\end_inset
@@ -7079,7 +7718,11 @@
\begin_layout Standard
As above.
- The depth of this phase change is specified by z_cmb.
+ The depth of this phase change is specified by
+\family typewriter
+z_cmb
+\family default
+.
\end_layout
\end_inset
@@ -7093,36 +7736,21 @@
\end_layout
\begin_layout Subsection
-Dimensional Information
+Momentum Equation Solver Parameters
\end_layout
\begin_layout Standard
\begin_inset Tabular
-<lyxtabular version="3" rows="1" columns="2">
+<lyxtabular version="3" rows="8" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
-<row topline="true" bottomline="true">
+<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-layerd=6371e3
-\newline
-density=3500.0
-\newline
-thermdiff=1.0e-6
-\newline
-gravacc=10.0
-\newline
-thermexp=3.0e-5
-\newline
-refvisc=1e21
-\newline
-cp
-=1250
-\newline
-wdensity=0.0
+stokes_flow_only=off
\end_layout
\end_inset
@@ -7131,48 +7759,116 @@
\begin_inset Text
\begin_layout Standard
-Various dimensional information.
-
+If you wish only to solve for the velocity once (e.g., Stokes flow) then make
+ this parameter on.
+ However, if you want to do a convection problem then this should be off.
\end_layout
\end_inset
</cell>
</row>
-</lyxtabular>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+\begin_layout Standard
+Solver=cgrad
+\end_layout
+
\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+\begin_layout Standard
+Can be either
+\begin_inset Quotes sld
+\end_inset
+cgrad
+\begin_inset Quotes srd
+\end_inset
+
+ for conjugate gradient solver or
+\begin_inset Quotes sld
+\end_inset
+
+multigrid
+\begin_inset Quotes srd
+\end_inset
+
+ for multigrid solver for the outer loop of the momentum solver.
\end_layout
-\begin_layout Subsection
-Data input and program debugging
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+node_assemble=on
\end_layout
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
\begin_layout Standard
-\begin_inset Tabular
-<lyxtabular version="3" rows="3" columns="2">
-<features islongtable="true">
-<column alignment="left" valignment="top" leftline="true" width="1.75in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+Whether to assemble stiffness matrix at the node level or not.
+\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
-DESCRIBE=off BEGINNER=off
+mg_cycle=1
\newline
-VERBOSE=off
+down_heavy=3
+\newline
+up_heavy=3
+\newline
+vlowstep=1000
+\newline
+vhighstep=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
-These parameters affect the echo behavior of the CitComS parser.
+Multigrid parameters.
+\family typewriter
+mg_cycle
+\family default
+=1 for V cycle and 2 for W cycle.
+
+\family typewriter
+down_heavy
+\family default
+ and
+\family typewriter
+up_heavy
+\family default
+ are the smoothing factors for downward/upward smoothing.
+
+\family typewriter
+vlowstep
+\family default
+ and
+\family typewriter
+vhighstep
+\family default
+ are the number of smoothing passes at lowest/highest levels.
\end_layout
\end_inset
@@ -7183,29 +7879,70 @@
\begin_inset Text
\begin_layout Standard
-verbose=off
+piterations=1000
\end_layout
\end_inset
</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Maximum iterations of the outer loop for momentum solver.
+\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
+accuracy=1.0e-6
+\newline
+tole_compressibility=1.0e-7
+\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 is used for debugging.
- If verbose is true, additional information is output to a .info file.
+Convergence criterion for momentum solver.
\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
+precond=on
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Whether to use the preconditioner
+\end_layout
+
+\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
-see_convergence=1
+aug_lagr=on aug_number=2.0e3
\end_layout
\end_inset
@@ -7214,8 +7951,8 @@
\begin_inset Text
\begin_layout Standard
-If see_convergence is true, the velocity residual will be output on the
- screen for every iteration.
+Whether to use augmented stiff matrix and the weight of the augmented stiff
+ matrix.
\end_layout
\end_inset
@@ -7229,12 +7966,12 @@
\end_layout
\begin_layout Subsection
-Solver Related Parameters
+Energy Equation Solver Parameters
\end_layout
\begin_layout Standard
\begin_inset Tabular
-<lyxtabular version="3" rows="10" columns="2">
+<lyxtabular version="3" rows="6" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -7243,15 +7980,7 @@
\begin_inset Text
\begin_layout Standard
-mg_cycle=1
-\newline
-down_heavy=3
-\newline
-up_heavy=3
-\newline
-vlowstep=2000
-\newline
-vhighstep=3
+ADV=on
\end_layout
\end_inset
@@ -7260,8 +7989,7 @@
\begin_inset Text
\begin_layout Standard
-Multigrid parameters.
-
+If on, solve the energy equation.
\end_layout
\end_inset
@@ -7272,7 +8000,7 @@
\begin_inset Text
\begin_layout Standard
-piterations=375
+fixed_timestep=0.0
\end_layout
\end_inset
@@ -7281,7 +8009,9 @@
\begin_inset Text
\begin_layout Standard
-Maximum iterations for momentum solver.
+If it is equal to 0, the size of time step is variable and is determined
+ dynamically.
+ Otherwise, the size of time step is fixed at the specified value.
\end_layout
\end_inset
@@ -7292,7 +8022,7 @@
\begin_inset Text
\begin_layout Standard
-accuracy=1.0e-6 tole_compressibility=1.0e-7
+finetunedt=0.9
\end_layout
\end_inset
@@ -7301,8 +8031,9 @@
\begin_inset Text
\begin_layout Standard
-Convergence criterion for momentum solver.
-
+Set the size of the time step to the specified fraction of maximum stable
+ advection time step.
+ Must be between 0 and 1.
\end_layout
\end_inset
@@ -7313,7 +8044,7 @@
\begin_inset Text
\begin_layout Standard
-ADV=on
+adv_sub_iterations=2
\end_layout
\end_inset
@@ -7322,18 +8053,18 @@
\begin_inset Text
\begin_layout Standard
-If true, solve energy equation.
+The number of iterations for energy solver.
\end_layout
\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
\begin_layout Standard
-fixed_timestep=0.0
+filter_temp=on
\end_layout
\end_inset
@@ -7342,20 +8073,18 @@
\begin_inset Text
\begin_layout Standard
-Set fixed time step.
- If it is 0, the size of time step is variable and is determined dynamically.
-
+Filter out the overshoots and undershoots of the temperature field or not.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-finetunedt=0.7
+inputdiffusivity=1
\end_layout
\end_inset
@@ -7364,18 +8093,36 @@
\begin_inset Text
\begin_layout Standard
-Set fraction of maximum advection time step.
+At this point, don't change the parameter.
+ It is used only in problems which are integrated backward in time.
\end_layout
\end_inset
</cell>
</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Age Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-adv_sub_iterations=2
+start_age=40.0
\end_layout
\end_inset
@@ -7384,18 +8131,76 @@
\begin_inset Text
\begin_layout Standard
-Set the number of iterations for energy solver.
+Set initial age (in Myrs).
+ This age determines which files of various time-dependent input to read
+ in.
+
\end_layout
\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
+reset_startage=off
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+If on, the initial age is set to
+\family typewriter
+start_age
+\family default
+.
+ If it is off and
+\family typewriter
+restart
+\family default
+ or
+\family typewriter
+post_p
+\family default
+ is on, the initial age is read in from previous output.
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Debugging Information
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="3" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-maxadvtime=10
+DESCRIBE=off
+\newline
+BEGINNER=off
+\newline
+VERBOSE=off
\end_layout
\end_inset
@@ -7404,7 +8209,8 @@
\begin_inset Text
\begin_layout Standard
-Maximum elapsed non-dimensional advection time.
+These parameters affect the echo behavior of the CitComS parser.
+ Only in none-pyre version.
\end_layout
\end_inset
@@ -7415,7 +8221,7 @@
\begin_inset Text
\begin_layout Standard
-precond=on
+verbose=off
\end_layout
\end_inset
@@ -7424,7 +8230,8 @@
\begin_inset Text
\begin_layout Standard
-Pre-conditioning flag.
+This is used for debugging.
+ If verbose is on, additional information is output to a .info file.
\end_layout
@@ -7436,7 +8243,7 @@
\begin_inset Text
\begin_layout Standard
-aug_lagr=on aug_number=2.0e3
+see_convergence=on
\end_layout
\end_inset
@@ -7445,7 +8252,8 @@
\begin_inset Text
\begin_layout Standard
-Augmented stiff matrix flag and value.
+If on, the velocity residual will be output on the screen for every iteration
+ of the momentum solver.
\end_layout
\end_inset
@@ -7459,12 +8267,12 @@
\end_layout
\begin_layout Subsection
-Age Information
+HDF5 Output Parameters
\end_layout
\begin_layout Standard
\begin_inset Tabular
-<lyxtabular version="3" rows="2" columns="2">
+<lyxtabular version="3" rows="4" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -7473,7 +8281,9 @@
\begin_inset Text
\begin_layout Standard
-start_age=40.0
+cb_block_size=1048576
+\newline
+cb_buffer_size=4194304
\end_layout
\end_inset
@@ -7482,20 +8292,69 @@
\begin_inset Text
\begin_layout Standard
-Set initial age (in Myrs).
- This age determines which vel_bound_file and mat_file to read in.
-
+Size for collective buffer in MPI-IO.
\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
+sieve_buf_size=1048576
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Size of data sieve buffer.
+\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
+output_alignment=262144
+\newline
+output_alignment_threshold=
+\newline
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+524288
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Memory alignment.
+\end_layout
+
+\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
-reset_startage=0
+cache_mdc_nelmts=10330
+\newline
+cache_rdcc_nelmts=521
+\newline
+cache_rdcc_nbytes=1048576
\end_layout
\end_inset
@@ -7504,10 +8363,7 @@
\begin_inset Text
\begin_layout Standard
-If reset_startage is true, the initial age is set to start_age.
- If it is false and restart or post_p is true, the initial age is read in
- from previous output.
-
+Cache size for chunked dataset.
\end_layout
\end_inset
@@ -7550,7 +8406,7 @@
\begin_inset Text
\begin_layout Standard
-These parameters control the resolution of spherical harmonics.
+These parameters control the resolution of the spherical harmonics.
Currently not used.
\end_layout
@@ -7565,30 +8421,121 @@
\end_layout
-\begin_layout Section
-CitComS.py Components
+\begin_layout Subsection
+Dimensional Information
\end_layout
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+layerd=6371e3
+\newline
+density=3500.0
+\newline
+thermdiff=1.0e-6
+\newline
+gravacc=10.0
+\newline
+thermexp=3.0e-5
+\newline
+refvisc=1.0e+21
+\newline
+
+cp=1250
+\newline
+wdensity=0.0
+\newline
+surftemp=273
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Various dimensional information in SI units.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
-launcher
+Required Information
\end_layout
\begin_layout Standard
-The Pyre facility
-\family typewriter
-\size footnotesize
-launcher
-\family default
-\size default
- controls how CitComS.py, an MPI application, is executed on multiple processors.
- It is the equivalent to
-\family typewriter
-mpirun
-\family default
- in MPI.
+\begin_inset Tabular
+<lyxtabular version="3" rows="1" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Problem=convection
+\newline
+Geometry=sphere
+\newline
+Spacing=regular
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+For this version of CitComS.py, all of these parameters must be set as indicated.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+CitComS.py Facilities and Properties
+\end_layout
+
+\begin_layout Standard
+This section lists the facilities and properties in the pyre version of
+ CitComS.py.
+ Most of the properties have identical names for the parameters as those
+ used in the none-pyre version of CitComS.py and is explained in the section
+ above.
+ This section highlights those which have changed and those which are entirely
+ new.
+ Parameters are given with their default values.
\end_layout
+\begin_layout Subsection
+Top-Level Facilities and Properties
+\end_layout
+
\begin_layout Standard
\noindent
\begin_inset Tabular
@@ -7601,7 +8548,7 @@
\begin_inset Text
\begin_layout Standard
-dry
+steps=1
\end_layout
\end_inset
@@ -7610,7 +8557,7 @@
\begin_inset Text
\begin_layout Standard
-If on, print command line and exit.
+How many time steps to run, including the 0-th time step.
\end_layout
\end_inset
@@ -7621,7 +8568,7 @@
\begin_inset Text
\begin_layout Standard
-nodegen
+launcher=mpich
\end_layout
\end_inset
@@ -7630,11 +8577,48 @@
\begin_inset Text
\begin_layout Standard
-A printf-style format string, used in conjunction with nodelist to generate
- list of machine names.
- Example:
-\family typewriter
-n%03d
+A facility specifying which launching command to use.
+ Choice includes:
+\begin_inset Quotes sld
+\end_inset
+
+mpich
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+lam-mpi
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+lsf
+\begin_inset Quotes srd
+\end_inset
+
+,
+\begin_inset Quotes sld
+\end_inset
+
+pbs
+\begin_inset Quotes srd
+\end_inset
+
+, and
+\begin_inset Quotes sld
+\end_inset
+
+globus
+\begin_inset Quotes srd
+\end_inset
+
+.
\end_layout
\end_inset
@@ -7645,7 +8629,7 @@
\begin_inset Text
\begin_layout Standard
-nodelist
+controller
\end_layout
\end_inset
@@ -7654,10 +8638,8 @@
\begin_inset Text
\begin_layout Standard
-A comma-separated list of machine names in square brackets.
- Example:
-\family typewriter
- [101-103,105,107]
+A facility.
+ User cannot change it.
\end_layout
\end_inset
@@ -7668,7 +8650,7 @@
\begin_inset Text
\begin_layout Standard
-machinefile
+solver=regional
\end_layout
\end_inset
@@ -7677,7 +8659,24 @@
\begin_inset Text
\begin_layout Standard
-Filename of machine file.
+A facility specifying which solver to use.
+ Must be either
+\begin_inset Quotes sld
+\end_inset
+
+regional
+\begin_inset Quotes srd
+\end_inset
+
+ or
+\begin_inset Quotes sld
+\end_inset
+
+full
+\begin_inset Quotes srd
+\end_inset
+
+.
\end_layout
\end_inset
@@ -7691,35 +8690,33 @@
\end_layout
\begin_layout Subsection
-journal
+launcher
\end_layout
\begin_layout Standard
-The Pyre facility
+The launcher facility controls how CitComS.py, an MPI application, is executed
+ on multiple processors.
+ It is the equivalent to
\family typewriter
-\size footnotesize
-journal
+mpirun
\family default
-\size default
- provides five types of debugging output for conceptually different types
- of information.
- The journal output stream can be instantiated as separated channels multiple
- times, and each channel can be individually activated or deactivated, and
- sent to different locations (the terminal, sockets, files, devices, etc.).
- The streams and their default states of the journal streams are:
-\newline
+ in MPI.
+
+\end_layout
+\begin_layout Standard
+\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="2">
+<lyxtabular version="3" rows="4" columns="2">
<features islongtable="true">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.75in">
-<column alignment="left" valignment="top" rightline="true" width="3.5in">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-debug
+dry=off
\end_layout
\end_inset
@@ -7728,7 +8725,7 @@
\begin_inset Text
\begin_layout Standard
-Filename of machine file.
+If on, print command line and exit without launching the job.
\end_layout
\end_inset
@@ -7739,7 +8736,7 @@
\begin_inset Text
\begin_layout Standard
-error
+nodegen
\end_layout
\end_inset
@@ -7748,31 +8745,20 @@
\begin_inset Text
\begin_layout Standard
-Unrecoverable runtime error.
- Default on.
-
-\end_layout
+A printf-styled format string, used in conjunction with
+\family typewriter
+nodelist
+\family default
+ to generate a list of machine names.
+ Example:
+\begin_inset Quotes sld
+\end_inset
+n%03d
+\begin_inset Quotes srd
\end_inset
-</cell>
-</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-\begin_layout Standard
-firewall
-\end_layout
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Fatal programming error.
- Default on.
-
\end_layout
\end_inset
@@ -7783,7 +8769,7 @@
\begin_inset Text
\begin_layout Standard
-info
+nodelist
\end_layout
\end_inset
@@ -7792,8 +8778,10 @@
\begin_inset Text
\begin_layout Standard
-Descriptive information.
- Default off.
+A comma-separated list of machine names in square brackets.
+ Example:
+\family typewriter
+ [101-103,105,107]
\end_layout
\end_inset
@@ -7804,7 +8792,7 @@
\begin_inset Text
\begin_layout Standard
-warning
+machinefile=mpirun.nodes
\end_layout
\end_inset
@@ -7813,8 +8801,10 @@
\begin_inset Text
\begin_layout Standard
-Recoverable runtime error.
- Default off.
+Filename of machine file.
+ Available only if
+\family typewriter
+launcher=mpich
\end_layout
\end_inset
@@ -7827,29 +8817,6 @@
\end_layout
-\begin_layout Standard
-The journal facility is not used in the uncoupled CitComS solver.
- For coupled solvers, there is a large amount of debugging information that
- outputs through the journal facility.
- That output can be turned on/off with command line options.
- The most important ones are
-\family typewriter
-journal.debug.Exchanger
-\family default
- and
-\family typewriter
-journal.debug.CitComSExchanger
-\family default
-.
- Try running the scripts with
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
---journal.debug.Exchanger=on --journal.debug.CitComSExchanger=on
-\end_layout
-
\begin_layout Subsection
controller
\end_layout
@@ -7865,7 +8832,7 @@
\begin_inset Text
\begin_layout Standard
-monitoringFrequency=100
+monitoringFrequency=10
\end_layout
\end_inset
@@ -7875,7 +8842,11 @@
\begin_layout Standard
The time step interval between disk output.
- It replaces the storage_spacing parameter in the (old) CitComS input file.
+ It replaces the
+\family typewriter
+storage_spacing
+\family default
+ parameter in the (old) CitComS input file.
\end_layout
\end_inset
@@ -7894,7 +8865,7 @@
\begin_layout Standard
\begin_inset Tabular
-<lyxtabular version="3" rows="16" columns="2">
+<lyxtabular version="3" rows="19" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -7912,8 +8883,30 @@
\begin_inset Text
\begin_layout Standard
-Can be either full-sphere or regional-sphere.
- It is set by the solver facility automatically.
+A facility.
+ Must be either
+\begin_inset Quotes sld
+\end_inset
+
+full-sphere
+\begin_inset Quotes srd
+\end_inset
+
+ or
+\begin_inset Quotes sld
+\end_inset
+
+regional-sphere
+\begin_inset Quotes srd
+\end_inset
+
+.
+ User does not need to specify it.
+ It is set by the
+\family typewriter
+solver
+\family default
+ facility automatically.
\end_layout
@@ -7934,7 +8927,7 @@
\begin_inset Text
\begin_layout Standard
-A temperature solver using Petrov-Galerkin time integration.
+A facility for the temperature solver using Petrov-Galerkin time integration.
\end_layout
@@ -7955,7 +8948,8 @@
\begin_inset Text
\begin_layout Standard
-A velocity solver using Boussinesq approximation and Uzawa algorithm.
+A facility for the velocity solver using Boussinesq approximation and Uzawa
+ algorithm.
\end_layout
@@ -7976,7 +8970,7 @@
\begin_inset Text
\begin_layout Standard
-Boundary conditions.
+A facility of boundary conditions.
\end_layout
\end_inset
@@ -7996,7 +8990,7 @@
\begin_inset Text
\begin_layout Standard
-Dimensional constants.
+A facility for dimensional constants.
\end_layout
\end_inset
@@ -8016,7 +9010,7 @@
\begin_inset Text
\begin_layout Standard
-Initial conditions.
+A facility for initial conditions.
\end_layout
\end_inset
@@ -8027,6 +9021,26 @@
\begin_inset Text
\begin_layout Standard
+output
+\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 output options.
+\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
param
\end_layout
@@ -8036,7 +9050,7 @@
\begin_inset Text
\begin_layout Standard
-Some additional input parameter files.
+A facility for some additional input parameter files.
\end_layout
\end_inset
@@ -8056,7 +9070,7 @@
\begin_inset Text
\begin_layout Standard
-Phase change.
+A facility for phase change parameters.
\end_layout
\end_inset
@@ -8076,7 +9090,7 @@
\begin_inset Text
\begin_layout Standard
-Viscosity.
+A facility for viscosity parameters.
\end_layout
\end_inset
@@ -8087,16 +9101,52 @@
\begin_inset Text
\begin_layout Standard
-datafile
+datadir=
+\begin_inset Quotes srd
+\end_inset
+
+.
+\begin_inset Quotes srd
+\end_inset
+
+
\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
+datafile=
+\begin_inset Quotes srd
+\end_inset
+
+regtest
+\begin_inset Quotes srd
+\end_inset
+
+
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-default="regtest"
+
\end_layout
\end_inset
@@ -8107,16 +9157,52 @@
\begin_inset Text
\begin_layout Standard
-datafile_old
+datadir_old=
+\begin_inset Quotes srd
+\end_inset
+
+.
+\begin_inset Quotes srd
+\end_inset
+
+
\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
+datafile_old=
+\begin_inset Quotes srd
+\end_inset
+
+regtest
+\begin_inset Quotes srd
+\end_inset
+
+
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-default="regtest"
+
\end_layout
\end_inset
@@ -8127,7 +9213,7 @@
\begin_inset Text
\begin_layout Standard
-rayleigh
+rayleigh=100000
\end_layout
\end_inset
@@ -8136,7 +9222,7 @@
\begin_inset Text
\begin_layout Standard
-default=1e+08
+
\end_layout
\end_inset
@@ -8147,7 +9233,7 @@
\begin_inset Text
\begin_layout Standard
-Q0 =0
+Q0=0
\end_layout
\end_inset
@@ -8167,7 +9253,7 @@
\begin_inset Text
\begin_layout Standard
-stokes_flow_only =0
+stokes_flow_only=off
\end_layout
\end_inset
@@ -8187,7 +9273,7 @@
\begin_inset Text
\begin_layout Standard
-verbos =0
+verbose=off
\end_layout
\end_inset
@@ -8207,7 +9293,7 @@
\begin_inset Text
\begin_layout Standard
-see_convergence =1
+see_convergence=on
\end_layout
\end_inset
@@ -8234,10 +9320,6 @@
\end_layout
\begin_layout Standard
-Available properties and default values include:
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="20" columns="2">
@@ -8249,7 +9331,7 @@
\begin_inset Text
\begin_layout Standard
-nproc_surf=1
+nproc_surf=1 or 12
\end_layout
\end_inset
@@ -8258,7 +9340,8 @@
\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
@@ -8329,7 +9412,7 @@
\begin_inset Text
\begin_layout Standard
-coor=0
+coor=off
\end_layout
\end_inset
@@ -8489,7 +9572,7 @@
\begin_inset Text
\begin_layout Standard
-theta_min=1.5
+theta_min=1.0708
\end_layout
\end_inset
@@ -8509,7 +9592,7 @@
\begin_inset Text
\begin_layout Standard
-theta_max=1.8
+theta_max=2.0708
\end_layout
\end_inset
@@ -8549,7 +9632,7 @@
\begin_inset Text
\begin_layout Standard
-fi_max=0.4
+fi_max=1
\end_layout
\end_inset
@@ -8656,13 +9739,9 @@
\end_layout
\begin_layout Standard
-Available properties and default values include:
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="8" columns="2">
+<lyxtabular version="3" rows="6" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -8671,7 +9750,7 @@
\begin_inset Text
\begin_layout Standard
-inputdiffusivity=1
+ADV=on
\end_layout
\end_inset
@@ -8691,7 +9770,7 @@
\begin_inset Text
\begin_layout Standard
-ADV=1
+filter_temp=on
\end_layout
\end_inset
@@ -8711,7 +9790,7 @@
\begin_inset Text
\begin_layout Standard
-fixed_timestep=0
+finetunedt=0.9
\end_layout
\end_inset
@@ -8731,7 +9810,7 @@
\begin_inset Text
\begin_layout Standard
-finetunedt=0.9
+fixed_timestep=0.0
\end_layout
\end_inset
@@ -8751,7 +9830,7 @@
\begin_inset Text
\begin_layout Standard
-adv_sub_iterations=2
+inputdiffusivity=1
\end_layout
\end_inset
@@ -8766,12 +9845,12 @@
\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
\begin_layout Standard
-maxadvtime=10
+adv_sub_iterations=2
\end_layout
\end_inset
@@ -8786,12 +9865,30 @@
\end_inset
</cell>
</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+solver.vsolver
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="13" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-aug_lagr=1
+Solver=cgrad
\end_layout
\end_inset
@@ -8806,12 +9903,12 @@
\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
\begin_layout Standard
-aug_number=2000
+node_assemble=on
\end_layout
\end_inset
@@ -8826,34 +9923,32 @@
\end_inset
</cell>
</row>
-</lyxtabular>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
-\end_inset
-
-
+\begin_layout Standard
+precond=on
\end_layout
-\begin_layout Subsection
-solver.vsolver
-\end_layout
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
\begin_layout Standard
-Available properties and default values include:
+
\end_layout
-\begin_layout Standard
-\noindent
-\begin_inset Tabular
-<lyxtabular version="3" rows="10" columns="2">
-<features islongtable="true">
-<column alignment="left" valignment="top" leftline="true" width="1.75in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
+\end_inset
+</cell>
+</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-node_assemble=1
+accuracy=1e-06
\end_layout
\end_inset
@@ -8873,7 +9968,7 @@
\begin_inset Text
\begin_layout Standard
-precond=1
+tole_compressibility=1e-07
\end_layout
\end_inset
@@ -8893,7 +9988,7 @@
\begin_inset Text
\begin_layout Standard
-accuracy=1e-06
+mg_cycle=1
\end_layout
\end_inset
@@ -8913,7 +10008,7 @@
\begin_inset Text
\begin_layout Standard
-tole_compressibility=1e-07
+down_heavy=3
\end_layout
\end_inset
@@ -8933,7 +10028,7 @@
\begin_inset Text
\begin_layout Standard
-mg_cycle=1
+up_heavy=3
\end_layout
\end_inset
@@ -8953,7 +10048,7 @@
\begin_inset Text
\begin_layout Standard
-down_heavy=3
+vlowstep=1000
\end_layout
\end_inset
@@ -8973,7 +10068,7 @@
\begin_inset Text
\begin_layout Standard
-up_heavy=3
+vhighstep=3
\end_layout
\end_inset
@@ -8993,7 +10088,7 @@
\begin_inset Text
\begin_layout Standard
-vlowstep=1000
+piterations=1000
\end_layout
\end_inset
@@ -9013,7 +10108,7 @@
\begin_inset Text
\begin_layout Standard
-vhighstep=3
+aug_lagr=on
\end_layout
\end_inset
@@ -9033,7 +10128,7 @@
\begin_inset Text
\begin_layout Standard
-piterations=1000
+aug_number=2000
\end_layout
\end_inset
@@ -9060,14 +10155,9 @@
\end_layout
\begin_layout Standard
-Available properties and default values are 0, 1, or 2 (open top).
- You cannot use "yes" or "no" for these values.
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="14" columns="2">
+<lyxtabular version="3" rows="15" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -9076,7 +10166,7 @@
\begin_inset Text
\begin_layout Standard
-side_sbcs=0
+side_sbcs=off
\end_layout
\end_inset
@@ -9096,6 +10186,26 @@
\begin_inset Text
\begin_layout Standard
+pseudo_free_surf=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
topvbc=0
\end_layout
@@ -9296,7 +10406,7 @@
\begin_inset Text
\begin_layout Standard
-temperature_bound_adj=0
+temperature_bound_adj=off
\end_layout
\end_inset
@@ -9363,10 +10473,6 @@
\end_layout
\begin_layout Standard
-Available properties and default values include:
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
@@ -9558,7 +10664,7 @@
\begin_inset Text
\begin_layout Standard
-depth_lith=89000
+z_lith=0.014
\end_layout
\end_inset
@@ -9578,7 +10684,7 @@
\begin_inset Text
\begin_layout Standard
-depth_410=410000
+z_410=0.06435
\end_layout
\end_inset
@@ -9598,7 +10704,7 @@
\begin_inset Text
\begin_layout Standard
-depth_660=660000
+z_lmantle=0.105
\end_layout
\end_inset
@@ -9618,7 +10724,7 @@
\begin_inset Text
\begin_layout Standard
-depth_cmb=2.691e+06
+z_cmb=0.439
\end_layout
\end_inset
@@ -9645,10 +10751,6 @@
\end_layout
\begin_layout Standard
-Available properties and default values include:
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="9" columns="2">
@@ -9660,7 +10762,7 @@
\begin_inset Text
\begin_layout Standard
-restart=0
+restart=off
\end_layout
\end_inset
@@ -9680,7 +10782,7 @@
\begin_inset Text
\begin_layout Standard
-post_p=0
+post_p=off
\end_layout
\end_inset
@@ -9720,7 +10822,7 @@
\begin_inset Text
\begin_layout Standard
-zero_elapsed_time=1
+zero_elapsed_time=on
\end_layout
\end_inset
@@ -9843,17 +10945,12 @@
\end_layout
\begin_layout Subsection
-solver.param
+solver.output
\end_layout
\begin_layout Standard
-Available properties and default values include:
-\end_layout
-
-\begin_layout Standard
-\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="13" columns="2">
+<lyxtabular version="3" rows="10" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -9862,7 +10959,15 @@
\begin_inset Text
\begin_layout Standard
-file_vbcs=0
+output_format=
+\begin_inset Quotes srd
+\end_inset
+
+ascii-local
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -9882,11 +10987,164 @@
\begin_inset Text
\begin_layout Standard
-vel_bound_file="bvel.dat"
+output_optional=
+\begin_inset Quotes srd
+\end_inset
+
+surf,botm
+\begin_inset Quotes srd
+\end_inset
+
+
\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
+cb_block_size=1048576
+\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
+cb_buffer_size=4194304
+\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
+sieve_buf_size=1048576
+\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
+output_alignment=262144
+\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
+output_alignment_threshold=
+\newline
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+524288
+\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
+cache_mdc_nelmts=10330
+\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
+cache_rdcc_nelmts=521
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
@@ -9897,12 +11155,50 @@
\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
+cache_rdcc_nbytes=1048576
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+solver.param
+\end_layout
+
+\begin_layout Standard
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="11" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
-mat_control=0
+file_vbcs=off
\end_layout
\end_inset
@@ -9922,7 +11218,7 @@
\begin_inset Text
\begin_layout Standard
-mat_file="mat.dat"
+vel_bound_file="bvel.dat"
\end_layout
\end_inset
@@ -9942,7 +11238,7 @@
\begin_inset Text
\begin_layout Standard
-lith_age=0
+mat_control=off
\end_layout
\end_inset
@@ -9962,7 +11258,7 @@
\begin_inset Text
\begin_layout Standard
-lith_age_file="age.dat"
+mat_file="mat.dat"
\end_layout
\end_inset
@@ -9982,7 +11278,7 @@
\begin_inset Text
\begin_layout Standard
-lith_age_time=0
+lith_age=off
\end_layout
\end_inset
@@ -10002,7 +11298,7 @@
\begin_inset Text
\begin_layout Standard
-lith_age_depth=0.0314
+lith_age_file="age.dat"
\end_layout
\end_inset
@@ -10022,7 +11318,7 @@
\begin_inset Text
\begin_layout Standard
-mantle_temp=1
+lith_age_time=off
\end_layout
\end_inset
@@ -10042,7 +11338,7 @@
\begin_inset Text
\begin_layout Standard
-tracer=0
+lith_age_depth=0.0314
\end_layout
\end_inset
@@ -10062,7 +11358,7 @@
\begin_inset Text
\begin_layout Standard
-tracer_file="tracer.dat"
+mantle_temp=1.0
\end_layout
\end_inset
@@ -10102,7 +11398,7 @@
\begin_inset Text
\begin_layout Standard
-reset_startage=0
+reset_startage=off
\end_layout
\end_inset
@@ -10129,10 +11425,6 @@
\end_layout
\begin_layout Standard
-Available properties and default values include:
-\end_layout
-
-\begin_layout Standard
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="12" columns="2">
@@ -10387,14 +11679,68 @@
\end_layout
\begin_layout Subsection
-solver.visc
+solver.tracer
\end_layout
\begin_layout Standard
-Available properties and default values include:
+\noindent
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.75in">
+<column alignment="left" valignment="top" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+tracer=off
\end_layout
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
\begin_layout Standard
+
+\end_layout
+
+\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
+tracer_file="tracer.dat"
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+solver.visc
+\end_layout
+
+\begin_layout Standard
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="16" columns="2">
@@ -10426,7 +11772,7 @@
\begin_inset Text
\begin_layout Standard
-rheol=3
+visc_smooth_method=3
\end_layout
\end_inset
@@ -10446,7 +11792,7 @@
\begin_inset Text
\begin_layout Standard
-visc_smooth_method=3
+VISC_UPDATE=on
\end_layout
\end_inset
@@ -10466,7 +11812,7 @@
\begin_inset Text
\begin_layout Standard
-VISC_UPDATE=on
+num_mat=4
\end_layout
\end_inset
@@ -10486,7 +11832,7 @@
\begin_inset Text
\begin_layout Standard
-num_mat=4
+visc0=1,1,1,1,
\end_layout
\end_inset
@@ -10506,7 +11852,7 @@
\begin_inset Text
\begin_layout Standard
-visc0=1,1,1,1,
+TDEPV=off
\end_layout
\end_inset
@@ -10526,7 +11872,7 @@
\begin_inset Text
\begin_layout Standard
-TDEPV=0
+rheol=3
\end_layout
\end_inset
@@ -10586,7 +11932,7 @@
\begin_inset Text
\begin_layout Standard
-SDEPV=0
+SDEPV=off
\end_layout
\end_inset
@@ -10646,7 +11992,7 @@
\begin_inset Text
\begin_layout Standard
-VMIN=0
+VMIN=off
\end_layout
\end_inset
@@ -10686,7 +12032,7 @@
\begin_inset Text
\begin_layout Standard
-VMAX=0
+VMAX=off
\end_layout
\end_inset
@@ -10725,9 +12071,172 @@
\end_inset
+
+\end_layout
+
+\begin_layout Subsection
+\noindent
+journal
+\end_layout
+
+\begin_layout Standard
+The Pyre facility
+\family typewriter
+\size footnotesize
+journal
+\family default
+\size default
+ provides five types of debugging output for conceptually different types
+ of information.
+ The journal output stream can be instantiated as separated channels multiple
+ times, and each channel can be individually activated or deactivated, and
+ sent to different locations (the terminal, sockets, files, devices, etc.).
+ The streams and their default states of the journal streams are:
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="2">
+<features islongtable="true">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.75in">
+<column alignment="left" valignment="top" rightline="true" width="3.5in">
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+debug
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Debugging information.
+ Default off.
+\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
+error
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Unrecoverable runtime error.
+ Default on.
\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
+firewall
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Fatal programming error.
+ Default on.
+
+\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
+info
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Descriptive information.
+ Default off.
+\end_layout
+
+\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
+warning
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Recoverable runtime error.
+ Default off.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The journal facility is not used in the uncoupled CitComS solver.
+ For coupled solvers, there is a large amount of debugging information that
+ outputs through the journal facility.
+ That output can be turned on/off with command line options.
+ The most important ones are
+\family typewriter
+journal.debug.Exchanger
+\family default
+ and
+\family typewriter
+journal.debug.CitComSExchanger
+\family default
+.
+ Try running the scripts with the following options:
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+--journal.debug.Exchanger=on --journal.debug.CitComSExchanger=on
+\end_layout
+
\begin_layout Chapter
CitComS.py Input File Format
\end_layout
@@ -11286,6 +12795,48 @@
topography heatflux vel_colat vel_lon
\end_layout
+\begin_layout Subsection
+Stress Output (test-case.stress.0.10)
+\end_layout
+
+\begin_layout Standard
+The first two lines are headers.
+ The rest of the file is column-based, where the meaning of each column
+ is:
+\end_layout
+
+\begin_layout LyX-Code
+Sxx Syy Szz Sxy Sxz Syz
+\end_layout
+
+\begin_layout Subsection
+Pressure Output (test-case.pressure.0.10)
+\end_layout
+
+\begin_layout Standard
+The first line is a header.
+ The rest of the file is column-based, where the meaning of each column
+ is:
+\end_layout
+
+\begin_layout LyX-Code
+pressure
+\end_layout
+
+\begin_layout Subsection
+Horizontal Average Output (test-case.average.0.10)
+\end_layout
+
+\begin_layout Standard
+The first line is a header.
+ The rest of the file is column-based, where the meaning of each column
+ is:
+\end_layout
+
+\begin_layout LyX-Code
+radius temperature RMS(V_horizontal) RMS(V_vertical)
+\end_layout
+
\begin_layout Section
HDF5 Output (test-case.h5)
\end_layout
More information about the cig-commits
mailing list