[cig-commits] [commit] python-removal: Removed section 2 from Appendix A of the manual, which describes the Pyre based parameters and settings. (4f1ae8b)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Fri Apr 11 16:28:47 PDT 2014
Repository : ssh://geoshell/citcoms
On branch : python-removal
Link : https://github.com/geodynamics/citcoms/compare/c23d985366bf195db41f383b779bc3aabb71808f...4f1ae8bee14cd6ca141f3914d231506c4db76e75
>---------------------------------------------------------------
commit 4f1ae8bee14cd6ca141f3914d231506c4db76e75
Author: Rajesh Kommu <rajesh.kommu at gmail.com>
Date: Wed Apr 9 09:28:32 2014 -0700
Removed section 2 from Appendix A of the manual, which describes the Pyre
based parameters and settings.
>---------------------------------------------------------------
4f1ae8bee14cd6ca141f3914d231506c4db76e75
doc/citcoms-manual.pdf | Bin 12616604 -> 12593603 bytes
doc/citcoms-manual.tex | 695 -------------------------------------------------
2 files changed, 695 deletions(-)
diff --git a/doc/citcoms-manual.pdf b/doc/citcoms-manual.pdf
index c4baae9..c9b7b58 100644
Binary files a/doc/citcoms-manual.pdf and b/doc/citcoms-manual.pdf differ
diff --git a/doc/citcoms-manual.tex b/doc/citcoms-manual.tex
index ea4bd88..2a88260 100644
--- a/doc/citcoms-manual.tex
+++ b/doc/citcoms-manual.tex
@@ -5691,701 +5691,6 @@ indicated.\tabularnewline
\hline
\end{tabular}
-
-\section{CitcomS Facilities and Properties}
-
-This section lists the facilities and properties in the Pyre version
-of CitcomS. Most of the properties have names which are identical
-to the parameters used in the non-Pyre version of CitcomS and are
-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.
-
-
-\subsection{Top-Level Facilities and Properties}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{steps=1}} & How many time steps to run.\tabularnewline
-\hline
-\texttt{\small{launcher=mpich}} & A facility specifying which launcher to use. Choices include \texttt{\small{mpich}}
-and \texttt{\small{lam-mpi}}.\tabularnewline
-\hline
-\texttt{\small{scheduler=none}} & A facility specifying which scheduler to use. Choices are \texttt{\small{lsf}},
-\texttt{\small{pbs}}, and \texttt{\small{globus}}.\tabularnewline
-\hline
-\texttt{\small{controller}} & A facility. User cannot change it.\tabularnewline
-\hline
-\texttt{\small{solver=regional}} & A facility specifying which solver to use. Must be either \texttt{\small{regional}}
-or \texttt{\small{full}}.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{launcher}}}
-
-The launcher facility controls how CitcomS, an MPI application, is
-executed on multiple processors. It is the equivalent to \texttt{mpirun}
-in MPI.
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{dry=off}} & If on, prints the \texttt{mpirun} command line and exits without launching
-the job.\tabularnewline
-\hline
-\texttt{\small{nodegen}} & A printf-styled format string, used in conjunction with \texttt{nodelist}
-to generate a list of machine names. Example: \texttt{\small{n\%03d}}\tabularnewline
-\hline
-\texttt{\small{nodelist}} & A comma-separated list of machine names in square brackets. Example:
-\texttt{ {[}101-103,105,107{]} }\tabularnewline
-\hline
-\texttt{\small{command}} & \texttt{The command used to launch the job. The default value should
-be customized if using any job scheduler, otherwise the default value
-should work well.}\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{scheduler}}}
-
-The scheduler facility controls how CitcomS submits jobs to a batch
-scheduler. Available schedulers include: \texttt{none} (default, not
-using a batch scheduler), \texttt{lsf} (for Load Sharing Facility
-batch scheduler), \texttt{pbs} (for Portable Batch System batch scheduler),
-\texttt{sge} (for Sun Grid Engine batch scheduler), and tacc-ranger
-(a variant of PBS, customized for the Ranger cluster at Texas Advanced
-Computing Center). Only the command options for these schedulers are
-listed below. For more information on configuring Pyre for your batch
-system, see CIG's Pythia page \url{geodynamics.org/cig/software/packages/cs/pythia/docs/batch}.
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{dry=off}} & If \texttt{\small{on}}, prints the batch script and exits without
-scheduling the job.\tabularnewline
-\hline
-\texttt{\small{wait=off}} & If \texttt{\small{on}}, waits for batch jobs to finish before exiting.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{job}}}
-
-The \texttt{\small{job}} facility controls options for individual
-batch jobs.
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{name}} & The name of the job.\tabularnewline
-\hline
-\texttt{\small{queue}} & The name of the queue to which the job is scheduled.\tabularnewline
-\hline
-\texttt{\small{walltime}} & Time limit for the job, specified using units, e.g., \texttt{5{*}minute},
-\texttt{2{*}hour}.\tabularnewline
-\hline
-\texttt{\small{stdin=/dev/null}} & File to read as the input stream.\tabularnewline
-\hline
-\texttt{\small{stdout=stdout.txt}} & File to write for the output stream.\tabularnewline
-\hline
-\texttt{\small{stderr=stderr.txt}} & File to write for the error stream.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{controller}}}
-
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{monitoringFrequency=100}} & The time-step interval between disk output. It replaces the \texttt{storage\_spacing}
-parameter in the (old) CitcomS input file.\tabularnewline
-\hline
-\texttt{\small{checkpointFrequency=100}} & The time-step interval between checkpoint output, which can be used
-later to resume the computation.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver }}}
-
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{mesher }} & A facility. Must be either \texttt{\small{full-sphere}} or \texttt{\small{regional-sphere}}.
-User does not need to specify it. It is set by the \texttt{solver}
-facility automatically. \tabularnewline
-\hline
-\texttt{\small{tsolver }} & A facility for the temperature solver using Petrov-Galerkin time integration. \tabularnewline
-\hline
-\texttt{\small{vsolver }} & A facility for the velocity solver using Boussinesq approximation
-and the Uzawa algorithm. \tabularnewline
-\hline
-\texttt{\small{bc }} & A facility of boundary conditions.\tabularnewline
-\hline
-\texttt{\small{const}} & A facility for dimensional constants.\tabularnewline
-\hline
-\texttt{\small{ic}} & A facility for initial conditions.\tabularnewline
-\hline
-\texttt{\small{output}} & A facility for output options.\tabularnewline
-\hline
-\texttt{\small{param}} & A facility for some additional input parameter files.\tabularnewline
-\hline
-\texttt{\small{phase }} & A facility for phase change parameters.\tabularnewline
-\hline
-\texttt{\small{tracer }} & A facility for tracer parameters.\tabularnewline
-\hline
-\texttt{\small{visc}} & A facility for viscosity parameters.\tabularnewline
-\hline
-\texttt{\small{datadir=\textquotedbl{}.\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{datafile=\textquotedbl{}regtest\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{datadir\_old=\textquotedbl{}.\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{datafile\_old=\textquotedbl{}regtest\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{rayleigh=100000}} & \tabularnewline
-\hline
-\texttt{\small{dissipation\_number=0.0}} & \tabularnewline
-\hline
-\texttt{\small{gruneisen=0.0}} & \tabularnewline
-\hline
-\texttt{\small{surfaceT=0.1}} & \tabularnewline
-\hline
-\texttt{\small{Q0=0}} & \tabularnewline
-\hline
-\texttt{\small{stokes\_flow\_only=off}} & \tabularnewline
-\hline
-\texttt{\small{verbose=off}} & \tabularnewline
-\hline
-\texttt{\small{see\_convergence=on}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.mesher}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{nprocx=1}} & \tabularnewline
-\hline
-\texttt{\small{nprocy=1}} & \tabularnewline
-\hline
-\texttt{\small{nprocz=1 }} & \tabularnewline
-\hline
-\texttt{\small{coor=0}} & \tabularnewline
-\hline
-\texttt{\small{coor\_file=\textquotedbl{}coor.dat\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{coor\_refine=0.1,0.15,0.1,0.2}} & \tabularnewline
-\hline
-\texttt{\small{nodex=9}} & \tabularnewline
-\hline
-\texttt{\small{nodey=9}} & \tabularnewline
-\hline
-\texttt{\small{nodez=9}} & \tabularnewline
-\hline
-\texttt{\small{levels=1 }} & \tabularnewline
-\hline
-\texttt{\small{radius\_outer=1}} & \tabularnewline
-\hline
-\texttt{\small{radius\_inner=0.55}} & \tabularnewline
-\hline
-\texttt{\small{theta\_min=1.0708}} & \tabularnewline
-\hline
-\texttt{\small{theta\_max=2.0708}} & \tabularnewline
-\hline
-\texttt{\small{fi\_min=0 }} & \tabularnewline
-\hline
-\texttt{\small{fi\_max=1}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.tsolver}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{ADV=on}} & \tabularnewline
-\hline
-\texttt{\small{filter\_temp=off}} & \tabularnewline
-\hline
-\texttt{\small{monitor\_max\_T=on}} & \tabularnewline
-\hline
-\texttt{\small{finetunedt=0.9}} & \tabularnewline
-\hline
-\texttt{\small{fixed\_timestep=0.0}} & \tabularnewline
-\hline
-\texttt{\small{inputdiffusivity=1}} & \tabularnewline
-\hline
-\texttt{\small{adv\_gamma=0.5}} & \tabularnewline
-\hline
-\texttt{\small{adv\_sub\_iterations=2}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.vsolver}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{Solver=cgrad}} & \tabularnewline
-\hline
-\texttt{\small{node\_assemble=on}} & \tabularnewline
-\hline
-\texttt{\small{precond=on}} & \tabularnewline
-\hline
-\texttt{\small{accuracy=1.0e-4}} & \tabularnewline
-\hline
-\texttt{\small{uzawa=cg}} & \tabularnewline
-\hline
-\texttt{\small{compress\_iter\_maxstep=100}} & \tabularnewline
-\hline
-\texttt{\small{mg\_cycle=1 }} & \tabularnewline
-\hline
-\texttt{\small{down\_heavy=3}} & \tabularnewline
-\hline
-\texttt{\small{up\_heavy=3}} & \tabularnewline
-\hline
-\texttt{\small{vlowstep=1000}} & \tabularnewline
-\hline
-\texttt{\small{vhighstep=3}} & \tabularnewline
-\hline
-\texttt{\small{max\_mg\_cycles=50}} & \tabularnewline
-\hline
-\texttt{\small{piterations=1000}} & \tabularnewline
-\hline
-\texttt{\small{aug\_lagr=on}} & \tabularnewline
-\hline
-\texttt{\small{aug\_number=2000}} & \tabularnewline
-\hline
-\texttt{\small{remove\_rigid\_rotation=on}} & \tabularnewline
-\hline
-\texttt{\small{remove\_angular\_momentum=on}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.bc }}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{side\_sbcs=off}} & \tabularnewline
-\hline
-\texttt{\small{pseudo\_free\_surf=off}} & \tabularnewline
-\hline
-\texttt{\small{topvbc=0}} & \tabularnewline
-\hline
-\texttt{\small{topvbxval=0}} & \tabularnewline
-\hline
-\texttt{\small{topvbyval=0}} & \tabularnewline
-\hline
-\texttt{\small{botvbc=0}} & \tabularnewline
-\hline
-\texttt{\small{botvbxval=0}} & \tabularnewline
-\hline
-\texttt{\small{botvbyval=0}} & \tabularnewline
-\hline
-\texttt{\small{toptbc=1}} & \tabularnewline
-\hline
-\texttt{\small{toptbcval=0}} & \tabularnewline
-\hline
-\texttt{\small{bottbc=1}} & \tabularnewline
-\hline
-\texttt{\small{bottbcval=1}} & \tabularnewline
-\hline
-\texttt{\small{temperature\_bound\_adj=off}} & \tabularnewline
-\hline
-\texttt{\small{depth\_bound\_adj=0.157}} & \tabularnewline
-\hline
-\texttt{\small{width\_bound\_adj=0.08727}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.const }}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{radius=6.371e+06}} & \tabularnewline
-\hline
-\texttt{\small{density=3340.0}} & \tabularnewline
-\hline
-\texttt{\small{thermdiff=1e-06}} & \tabularnewline
-\hline
-\texttt{\small{gravacc=9.81}} & \tabularnewline
-\hline
-\texttt{\small{thermexp=3e-05}} & \tabularnewline
-\hline
-\texttt{\small{refvisc=1e+21}} & \tabularnewline
-\hline
-\texttt{\small{cp=1200}} & \tabularnewline
-\hline
-\texttt{\small{density\_above=1030.0}} & \tabularnewline
-\hline
-\texttt{\small{density\_below=6600.0}} & \tabularnewline
-\hline
-\texttt{\small{z\_lith=0.014}} & \tabularnewline
-\hline
-\texttt{\small{z\_410=0.06435}} & \tabularnewline
-\hline
-\texttt{\small{z\_lmantle=0.105}} & \tabularnewline
-\hline
-\texttt{\small{z\_cmb=0.439}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.ic }}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{restart=off}} & \tabularnewline
-\hline
-\texttt{\small{post\_p=off}} & \tabularnewline
-\hline
-\texttt{\small{solution\_cycles\_init=0}} & \tabularnewline
-\hline
-\texttt{\small{zero\_elapsed\_time=on}} & \tabularnewline
-\hline
-\texttt{\small{tic\_method=0}} & \tabularnewline
-\hline
-\texttt{\small{num\_perturbations=1}} & \tabularnewline
-\hline
-\texttt{\small{perturbl=1}} & \tabularnewline
-\hline
-\texttt{\small{perturbm=1}} & \tabularnewline
-\hline
-\texttt{\small{perturblayer=5}} & \tabularnewline
-\hline
-\texttt{\small{perturbmag=0.05}} & \tabularnewline
-\hline
-\texttt{\small{half\_space\_age=40}} & \tabularnewline
-\hline
-\texttt{\small{mantle\_temp=1.0}} & \tabularnewline
-\hline
-\texttt{\small{blob\_center={[}-999,-999,-999{]} }} & \tabularnewline
-\hline
-\texttt{\small{blob\_radius=0.063 }} & \tabularnewline
-\hline
-\texttt{\small{blob\_dT=0.18}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.output}}}
-
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{output\_format=\textquotedbl{}ascii\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{output\_optional=\textquotedbl{}surf,botm,}}~\\
-\texttt{\small{tracer\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{output\_ll\_max=20}} & \tabularnewline
-\hline
-\texttt{self\_gravitation=off} & \tabularnewline
-\hline
-\texttt{use\_cbf\_topo=off} & \tabularnewline
-\hline
-\texttt{\small{cb\_block\_size=1048576}} & \tabularnewline
-\hline
-\texttt{\small{cb\_buffer\_size=4194304}} & \tabularnewline
-\hline
-\texttt{\small{sieve\_buf\_size=1048576}} & \tabularnewline
-\hline
-\texttt{\small{output\_alignment=262144}} & \tabularnewline
-\hline
-\texttt{\small{output\_alignment\_threshold=}}~\\
-\texttt{\small{~~~~524288}} & \tabularnewline
-\hline
-\texttt{\small{cache\_mdc\_nelmts=10330}} & \tabularnewline
-\hline
-\texttt{\small{cache\_rdcc\_nelmts=521}} & \tabularnewline
-\hline
-\texttt{\small{cache\_rdcc\_nbytes=1048576}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.param}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{reference\_state=1}} & \tabularnewline
-\hline
-\texttt{\small{refstate\_file=\textquotedbl{}refstate.dat\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{mineral\_physics\_model=3}} & \tabularnewline
-\hline
-\texttt{\small{file\_vbcs=off}} & \tabularnewline
-\hline
-\texttt{\small{vel\_bound\_file=\textquotedbl{}bvel.dat\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{mat\_control=off}} & \tabularnewline
-\hline
-\texttt{\small{mat\_file=\textquotedbl{}mat.dat\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{lith\_age=off}} & \tabularnewline
-\hline
-\texttt{\small{lith\_age\_file=\textquotedbl{}age.dat\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{lith\_age\_time=off}} & \tabularnewline
-\hline
-\texttt{\small{lith\_age\_depth=0.0314}} & \tabularnewline
-\hline
-\texttt{\small{start\_age=40 }} & \tabularnewline
-\hline
-\texttt{\small{reset\_startage=off}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.phase}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{Ra\_410=0 }} & \tabularnewline
-\hline
-\texttt{\small{clapeyron410=0.0235}} & \tabularnewline
-\hline
-\texttt{\small{transT410=0.78 }} & \tabularnewline
-\hline
-\texttt{\small{width410=0.0058}} & \tabularnewline
-\hline
-\texttt{\small{Ra\_670=0}} & \tabularnewline
-\hline
-\texttt{\small{clapeyron670=-0.0235}} & \tabularnewline
-\hline
-\texttt{\small{transT670=0.78}} & \tabularnewline
-\hline
-\texttt{\small{width670=0.0058}} & \tabularnewline
-\hline
-\texttt{\small{Ra\_cmb=0}} & \tabularnewline
-\hline
-\texttt{\small{clapeyroncmb=-0.0235}} & \tabularnewline
-\hline
-\texttt{\small{transTcmb=0.875}} & \tabularnewline
-\hline
-\texttt{\small{widthcmb=0.0058}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.tracer}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{tracer=off}} & \tabularnewline
-\hline
-\texttt{\small{tracer\_ic\_method=0}} & \tabularnewline
-\hline
-\texttt{\small{tracers\_per\_element=10}} & \tabularnewline
-\hline
-\texttt{\small{tracer\_file=\textquotedbl{}tracer.dat\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{tracer\_flavors=0}} & \tabularnewline
-\hline
-\texttt{\small{ic\_method\_for\_flavors=0}} & \tabularnewline
-\hline
-\texttt{\small{z\_interface=0.7}} & \tabularnewline
-\hline
-\texttt{\small{itracer\_warnings=on}} & \tabularnewline
-\hline
-\texttt{\small{regular\_grid\_deltheta=1.0}} & \tabularnewline
-\hline
-\texttt{\small{regular\_grid\_delphi=1.0}} & \tabularnewline
-\hline
-\texttt{\small{chemical\_buoyancy=on}} & \tabularnewline
-\hline
-\texttt{\small{buoy\_type=1}} & \tabularnewline
-\hline
-\texttt{\small{buoyancy\_ratio=1.0}} & \tabularnewline
-\hline
-\texttt{\small{tracer\_enriched=off}} & \tabularnewline
-\hline
-\texttt{\small{Q0\_enriched=0.0}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\texttt{\normalsize{solver.visc}}}
-
-\noindent %
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{Viscosity=\textquotedbl{}system\textquotedbl{}}} & \tabularnewline
-\hline
-\texttt{\small{visc\_smooth\_method=3}} & \tabularnewline
-\hline
-\texttt{\small{VISC\_UPDATE=on}} & \tabularnewline
-\hline
-\texttt{\small{num\_mat=4}} & \tabularnewline
-\hline
-\texttt{\small{visc0=1,1,1,1,}} & \tabularnewline
-\hline
-\texttt{\small{TDEPV=off}} & \tabularnewline
-\hline
-\texttt{\small{rheol=3}} & \tabularnewline
-\hline
-\texttt{\small{viscE=1,1,1,1,}} & \tabularnewline
-\hline
-\texttt{\small{viscT=1,1,1,1,}} & \tabularnewline
-\hline
-\texttt{\small{viscZ=1,1,1,1,}} & \tabularnewline
-\hline
-\texttt{\small{SDEPV=off}} & \tabularnewline
-\hline
-\texttt{\small{sdepv\_misfit=0.001}} & \tabularnewline
-\hline
-\texttt{\small{sdepv\_expt=1,1,1,1,}} & \tabularnewline
-\hline
-\texttt{\small{PDEPV=off}} & \tabularnewline
-\hline
-\texttt{\small{pdepv\_a=1e20,1e20,1e20,1e20}} & \tabularnewline
-\hline
-\texttt{\small{pdepv\_b=0,0,0,0}} & \tabularnewline
-\hline
-\texttt{\small{pdepv\_y=1e20,1e20,1e20,1e20}} & \tabularnewline
-\hline
-\texttt{\small{pdepv\_eff=on}} & \tabularnewline
-\hline
-\texttt{\small{pdepv\_offset=0}} & \tabularnewline
-\hline
-\texttt{\small{CDEPV=off}} & \tabularnewline
-\hline
-\texttt{\small{cdepv\_ff=1,1}} & \tabularnewline
-\hline
-\texttt{\small{low\_visc\_channel=0}} & \tabularnewline
-\hline
-\texttt{\small{low\_visc\_wedge=0}} & \tabularnewline
-\hline
-\texttt{\small{lv\_min\_radius=0.9764}} & \tabularnewline
-\hline
-\texttt{\small{lv\_max\_radius=0.9921}} & \tabularnewline
-\hline
-\texttt{\small{lv\_channel\_thickness=0.0047}} & \tabularnewline
-\hline
-\texttt{\small{lv\_reduction=0.5}} & \tabularnewline
-\hline
-\texttt{\small{VMIN=off}} & \tabularnewline
-\hline
-\texttt{\small{visc\_min=0.001}} & \tabularnewline
-\hline
-\texttt{\small{VMAX=off}} & \tabularnewline
-\hline
-\texttt{\small{visc\_max=1000}} & \tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\noindent \texttt{\normalsize{layout}}}
-
-The following facilities are only used in the coupled CitcomS solver.
-\\
-\\
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{containing\_group={[}0-11{]}}} & The processors to be assigned to the csolver.\tabularnewline
-\hline
-\texttt{\small{embedded\_group={[}12{]}}} & The processors to be assigned to the esolver.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\noindent \texttt{\normalsize{ccoupler}}}
-
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{si\_unit=off}} & Whether to exchange information in SI units.\tabularnewline
-\hline
-\texttt{\small{cartesian=off}} & Whether to exchange information in Cartesian coordinate.\tabularnewline
-\hline
-\texttt{\small{two\_way\_communication=on}} & Whether to transfer information from esolver to csolver.\tabularnewline
-\hline
-\texttt{\small{exchange\_initial\_temperature}}~\\
-\texttt{\small{=on}} & Whether to ensure consistent initial temperature between csolver or
-esolver.\tabularnewline
-\hline
-\texttt{\small{exchange\_pressure=on}} & Whether to send the pressure solution to esolver.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\noindent \texttt{\normalsize{ecoupler}}}
-
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{si\_unit=off}} & Whether to exchange information in SI units.\tabularnewline
-\hline
-\texttt{\small{cartesian=off}} & Whether to exchange information in Cartesian coordinate.\tabularnewline
-\hline
-\texttt{\small{two\_way\_communication=on}} & Whether to transfer information from esolver to csolver.\tabularnewline
-\hline
-\texttt{\small{exchange\_initial\_temperature=on}} & Whether to ensure consistent initial temperature between csolver or
-esolver.\tabularnewline
-\hline
-\texttt{\small{exchange\_pressure=on}} & Whether to receive the initial guess of pressure from csolver.\tabularnewline
-\hline
-\texttt{\small{exclude\_top=off}} & Whether to exclude the top boundary when receiving boundary conditions
-from the csolver. If the esolver has imposed plate velocity and constant
-temperature at the surface, set this to on.\tabularnewline
-\hline
-\texttt{\small{exclude\_bottom=off}} & Whether to exclude the bottom boundary when receiving boundary conditions
-from the csolver.\tabularnewline
-\hline
-\texttt{\small{amending\_outflow=off}} & Whether to amend the velocity boundary conditions to satisfy the continuity
-equation.\tabularnewline
-\hline
-\end{tabular}
-
-
-\subsection{\noindent \texttt{\normalsize{journal}}}
-
-The Pyre facility \texttt{journal} 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:\\
-\\
-\begin{tabular}{|>{\raggedright}p{1.85in}|>{\raggedright}p{4.25in}|}
-\hline
-\texttt{\small{debug}} & Debugging information. Default off.\tabularnewline
-\hline
-\texttt{\small{error}} & Unrecoverable runtime error. Default on. \tabularnewline
-\hline
-\texttt{\small{firewall}} & Fatal programming error. Default on. \tabularnewline
-\hline
-\texttt{\small{info}} & Descriptive information. Default off.\tabularnewline
-\hline
-\texttt{\small{warning}} & Recoverable runtime error. Default off.\tabularnewline
-\hline
-\end{tabular}\\
-\\
-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 \texttt{journal.debug.Exchanger}
-and \texttt{journal.debug.CitcomS-Exchanger}. Other less important
-options can be found in \texttt{tests/coupled.cfg}. To enable the
-journal output, try running the scripts with the following options:
-\begin{lyxcode}
-{[}CitcomS.journal.debug{]}~\\
-Exchanger~=~on~\\
-CitcomS-Exchanger~=~on
-\end{lyxcode}
-
\chapter{CitcomS Input File Format}
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