[cig-commits] r17237 - seismo/3D/SPECFEM3D/trunk/USER_MANUAL
pieyre at geodynamics.org
pieyre at geodynamics.org
Tue Oct 5 06:47:02 PDT 2010
Author: pieyre
Date: 2010-10-05 06:47:02 -0700 (Tue, 05 Oct 2010)
New Revision: 17237
Modified:
seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.pdf
seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex
Log:
modified the section 'meshfem3D' of the manual
Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.pdf
===================================================================
(Binary files differ)
Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex
===================================================================
--- seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex 2010-10-04 20:20:38 UTC (rev 17236)
+++ seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex 2010-10-05 13:47:02 UTC (rev 17237)
@@ -282,13 +282,12 @@
\par\end{flushleft}
-You are now ready to compile the mesher. In the directory with the
-source code type `\texttt{make meshfem3D}'. If all paths and flags
+You are now ready to compile the mesher. In the directory \texttt{meshfem3D} type `\texttt{make meshfem3D}'. If all paths and flags
have been set correctly, the mesher should now compile and produce
the executable \texttt{xmeshfem3D}.
-Input for the mesher (and the solver) is provided through the parameter
-file \texttt{Par\_file}, which resides in the subdirectory \texttt{DATA}.
+Input for the mesher is provided through the parameter
+file \texttt{Par\_file}, which resides in the subdirectory \texttt{meshfem3D/DATA}.
Before running the mesher, a number of parameters need to be set in
the \texttt{Par\_file}. This requires a basic understanding of how
the SEM is implemented, and we encourage you to read \citet{KoVi98,KoTr99}
@@ -307,14 +306,14 @@
the \texttt{Par\_file}:
\begin{description}
-\item [{\texttt{SIMULATION\_TYPE}}] is set to 1 for forward simulations,
-2 for adjoint simulations (see Section \ref{sec:Adjoint-simulation-finite})
-and 3 for kernel simulations (see Section \ref{sec:Finite-Frequency-Kernels}).
-\item [{\texttt{SAVE\_FORWARD}}] is only set to \texttt{.true.} for a forward
-simulation with the last frame of the simulation saved, as part of
-the finite-frequency kernel calculations (see Section \ref{sec:Finite-Frequency-Kernels}).
-For a regular forward simulation, leave \texttt{SIMULATION\_TYPE}
-and \texttt{SAVE\_FORWARD} at their default values.
+%% \item [{\texttt{SIMULATION\_TYPE}}] is set to 1 for forward simulations,
+%% 2 for adjoint simulations (see Section \ref{sec:Adjoint-simulation-finite})
+%% and 3 for kernel simulations (see Section \ref{sec:Finite-Frequency-Kernels}).
+%% \item [{\texttt{SAVE\_FORWARD}}] is only set to \texttt{.true.} for a forward
+%% simulation with the last frame of the simulation saved, as part of
+%% the finite-frequency kernel calculations (see Section \ref{sec:Finite-Frequency-Kernels}).
+%% For a regular forward simulation, leave \texttt{SIMULATION\_TYPE}
+%% and \texttt{SAVE\_FORWARD} at their default values.
\item [{\texttt{LATITUDE\_MIN}}] Minimum latitude in the block (negative
for South).
\item [{\texttt{LATITUDE\_MAX}}] Maximum latitude in the block.
@@ -322,6 +321,18 @@
for West).
\item [{\texttt{LONGITUDE\_MAX}}] Maximum longitude in the block.
\item [{\texttt{DEPTH\_BLOCK\_KM}}] Depth of bottom of mesh in kilometers.
+\item [{\texttt{\noun{UTM\_PROJECTION\_ZONE}}}] UTM projection zone in
+which your model resides, only valid when \texttt{SUPPRESS\_UTM\_}~\\
+\texttt{PROJECTION} is \texttt{.false.}.
+\item [{\texttt{SUPPRESS\_UTM\_PROJECTION}}] set to be \texttt{.false.}
+when your model range is specified in the geographical coordinates,
+and needs to be \texttt{.true.} when your model is specified in a
+cartesian coordinates. \noun{UTM projection zone in which your simulation
+region resides.}
+\item [{\texttt{INTERFACES\_FILE }}] File in which contains the description of the topography and
+of the interfaces between the different layers of the model, if any.
+The number of spectral elements in the vertical direction within each layer is also defined in this file.
+
\item [{$\nexxi$}] The number of spectral elements along one side of the
block. This number \textit{must} be 8~$\times$~a multiple of $\nprocxi$
defined below. Based upon benchmarks against semi-analytical discrete
@@ -337,14 +348,14 @@
by \texttt{NGLLX} in the \texttt{constants.h} file. We generally use
$\mbox{\texttt{NGLLX\/}}=5$, for a total of $5^{3}=125$ points per
elements. We suggest not to change this value.
-\item [{\texttt{\noun{UTM\_PROJECTION\_ZONE}}}] UTM projection zone in
-which your model resides, only valid when \texttt{SUPPRESS\_UTM\_}~\\
-\texttt{PROJECTION} is \texttt{.false.}.
-\item [{\texttt{SUPPRESS\_UTM\_PROJECTION}}] set to be \texttt{.false.}
-when your model range is specified in the geographical coordinates,
-and needs to be \texttt{.true.} when your model is specified in a
-cartesian coordinates. \noun{UTM projection zone in which your simulation
-region resides.}
+%% \item [{\texttt{\noun{UTM\_PROJECTION\_ZONE}}}] UTM projection zone in
+%% which your model resides, only valid when \texttt{SUPPRESS\_UTM\_}~\\
+%% \texttt{PROJECTION} is \texttt{.false.}.
+%% \item [{\texttt{SUPPRESS\_UTM\_PROJECTION}}] set to be \texttt{.false.}
+%% when your model range is specified in the geographical coordinates,
+%% and needs to be \texttt{.true.} when your model is specified in a
+%% cartesian coordinates. \noun{UTM projection zone in which your simulation
+%% region resides.}
\item [{$\nexeta$}] The number of spectral elements along the other side
of the block. This number \textit{must} be 8~$\times$~a multiple
of $\nproceta$ defined below.
@@ -355,73 +366,88 @@
\item [{$\nproceta$}] The number of processors or slices along the other
side of the block; we must have $\nexeta=8\times c\times\nproceta$,
where $c\ge1$ is a positive integer.
-\item [{\texttt{MODEL}}] Must be set to one of the following:
+\item [{\texttt{USE\_REGULAR\_MESH}}] set to be \texttt{.true.} if you want a perfectly regular
+mesh or \texttt{.false.} if you want to add doubling horizontal layers to coarsen the mesh. In this case, you
+also need to provide additional information by setting up the next three parameters.
+\item [{\texttt{NDOUBLINGS}}] The number of horizontal doubling layers. Must be set to \texttt{1} or \texttt{2}
+if \texttt{USE\_REGULAR\_MESH} is set to \texttt{.true.}.
+\item [{\texttt{NZ\_DOUBLING\_1}}] The position of the first doubling layer (only interpreted
+if \texttt{USE\_REGULAR\_MESH} is set to \texttt{.true.}).
+\item [{\texttt{NZ\_DOUBLING\_2}}] The position of the second doubling layer (only interpreted
+if \texttt{USE\_REGULAR\_MESH} is set to \texttt{.true.} and if \texttt{NDOUBLINGS} is set to \texttt{2}).
-\begin{description}
-\item [{\texttt{SoCal}}] Isotropic, southern California layercake model
-developed by \citet{DrHe90}.
-\item [{\texttt{Harvard\_LA}}] 3D model based upon the high-resolution
-Los Angeles basin model developed by \citet{SuSh03} the Salton Trough
-model developed by \citet{lovelyetal06}, the regional tomographic
-model of \citet{hauksson2000}, and the Moho map determined by \citet{zhu&kanamori2000}.
-\end{description}
-\item [{\texttt{OCEANS}}] Set to \texttt{.true.} if the effect of the oceans
-on seismic wave propagation should be incorporated based upon the
-approximate treatment discussed in \citet{KoTr02b}. This feature
-is inexpensive from a numerical perspective, both in terms of memory
-requirements and CPU time. This approximation is accurate at periods
-of roughly 20~s and longer. At shorter periods the effect of water
-phases/reverberations is not taken into account, even when the flag
-is on.
-\item [{\texttt{TOPOGRAPHY}}] Set to \texttt{.true.} if topography and
-bathymetry should be incorporated based upon model ETOPO5 \citep{Etopo5}.
-This feature adds no cost to the simulation.
-\item [{\texttt{ATTENUATION}}] Set to \texttt{.true.} if attenuation should
-be incorporated. Turning this feature on increases the memory requirements
-significantly (roughly by a factor of~1.5), and is numerically fairly
-expensive. See \citet{KoTr99,KoTr02a} for a discussion on the implementation
-of attenuation based upon standard linear solids.
-\item [{\texttt{USE\_OLSEN\_ATTENUATION}}] Set to \texttt{.true.} if you
-want to use the attenuation model that scaled from the velocity model
-using Olsen's empirical relation (reference).
-\item [{\texttt{ABSORBING\_CONDITIONS}}] Set to \texttt{.true.} to turn
-on Clayton-Enquist absorbing boundary conditions (see \citet{KoTr99}).
-\item [{\texttt{RECORD\_LENGTH\_IN\_MINUTES}}] Choose the desired record
-length of the synthetic seismograms (in minutes). This controls the
-length of the numerical simulation, i.e., twice the record length
-requires twice as much CPU time. This feature is not used at the time
-of meshing but is required for the solver, i.e., you may change this
-parameter after running the mesher.
-\item [{\texttt{MOVIE\_SURFACE}}] Set to \texttt{.false.}, unless you want
-to create a movie of seismic wave propagation on the Earth's surface.
-Turning this option on generates large output files. See Section \ref{sec:Movies}
-for a discussion on the generation of movies. This feature is not
-used at the time of meshing but is relevant for the solver.
-\item [{\texttt{MOVIE\_VOLUME}}] Set to \texttt{.false.}, unless you want
-to create a movie of seismic wave propagation in the Earth's interior.
-Turning this option on generates huge output files. See Section \ref{sec:Movies}
-for a discussion on the generation of movies. This feature is not
-used at the time of meshing but is relevant for the solver.
-\item [{\texttt{NTSTEP\_BETWEEN\_FRAMES}}] Determines the number of timesteps
-between movie frames. Typically you want to save a snapshot every
-100 timesteps. The smaller you make this number the more output will
-be generated! See Section \ref{sec:Movies} for a discussion on the
-generation of movies. This feature is not used at the time of meshing
-but is relevant for the solver.
-\item [{\texttt{CREATE\_SHAKEMAP}}] Set this flag to \texttt{.true.} to
-create a ShakeMap\textregistered, i.e., a peak ground velocity map
-of the maximum absolute value of the two horizontal components of the velocity vector.
-\item [{\texttt{SAVE\_DISPLACEMENT}}] Set this flag to \texttt{.true.}
-if you want to save the displacement instead of velocity for the movie
-frames.
-\item [{\texttt{USE\_HIGHRES\_FOR\_MOVIES}}] Set this flag to \texttt{.true.}
-if you want to save the values at all the NGLL grid points for the
-movie frames.
-\item [{\texttt{SAVE\_MESH\_FILES}}] Set this flag to \texttt{.true.} to
-save AVS \url{www.avs.com}, OpenDX \url{www.opendx.org}, or ParaView \url{www.paraview.org}
-mesh files for subsequent viewing. Turning the flag on generates large
-(distributed) files in the \texttt{LOCAL\_PATH} directory. See Section~\ref{sec:Mesh-graphics}
-for a discussion of mesh viewing features.
+%%\item [{\texttt{MODEL}}] Must be set to one of the following:
+%%\begin{description}
+%% \item [{\texttt{SoCal}}] Isotropic, southern California layercake model
+%% developed by \citet{DrHe90}.
+%% \item [{\texttt{Harvard\_LA}}] 3D model based upon the high-resolution
+%% Los Angeles basin model developed by \citet{SuSh03} the Salton Trough
+%% model developed by \citet{lovelyetal06}, the regional tomographic
+%% model of \citet{hauksson2000}, and the Moho map determined by \citet{zhu&kanamori2000}.
+%% \end{description}
+%% \item [{\texttt{OCEANS}}] Set to \texttt{.true.} if the effect of the oceans
+%% on seismic wave propagation should be incorporated based upon the
+%% approximate treatment discussed in \citet{KoTr02b}. This feature
+%% is inexpensive from a numerical perspective, both in terms of memory
+%% requirements and CPU time. This approximation is accurate at periods
+%% of roughly 20~s and longer. At shorter periods the effect of water
+%% phases/reverberations is not taken into account, even when the flag
+%% is on.
+%% \item [{\texttt{TOPOGRAPHY}}] Set to \texttt{.true.} if topography and
+%% bathymetry should be incorporated based upon model ETOPO5 \citep{Etopo5}.
+%% This feature adds no cost to the simulation.
+%% \item [{\texttt{ATTENUATION}}] Set to \texttt{.true.} if attenuation should
+%% be incorporated. Turning this feature on increases the memory requirements
+%% significantly (roughly by a factor of~1.5), and is numerically fairly
+%% expensive. See \citet{KoTr99,KoTr02a} for a discussion on the implementation
+%% of attenuation based upon standard linear solids.
+%% \item [{\texttt{USE\_OLSEN\_ATTENUATION}}] Set to \texttt{.true.} if you
+%% want to use the attenuation model that scaled from the velocity model
+%% using Olsen's empirical relation (reference).
+%% \item [{\texttt{ABSORBING\_CONDITIONS}}] Set to \texttt{.true.} to turn
+%% on Clayton-Enquist absorbing boundary conditions (see \citet{KoTr99}).
+%% \item [{\texttt{RECORD\_LENGTH\_IN\_MINUTES}}] Choose the desired record
+%% length of the synthetic seismograms (in minutes). This controls the
+%% length of the numerical simulation, i.e., twice the record length
+%% requires twice as much CPU time. This feature is not used at the time
+%% of meshing but is required for the solver, i.e., you may change this
+%% parameter after running the mesher.
+%% \item [{\texttt{MOVIE\_SURFACE}}] Set to \texttt{.false.}, unless you want
+%% to create a movie of seismic wave propagation on the Earth's surface.
+%% Turning this option on generates large output files. See Section \ref{sec:Movies}
+%% for a discussion on the generation of movies. This feature is not
+%% used at the time of meshing but is relevant for the solver.
+%% \item [{\texttt{MOVIE\_VOLUME}}] Set to \texttt{.false.}, unless you want
+%% to create a movie of seismic wave propagation in the Earth's interior.
+%% Turning this option on generates huge output files. See Section \ref{sec:Movies}
+%% for a discussion on the generation of movies. This feature is not
+%% used at the time of meshing but is relevant for the solver.
+%% \item [{\texttt{NTSTEP\_BETWEEN\_FRAMES}}] Determines the number of timesteps
+%% between movie frames. Typically you want to save a snapshot every
+%% 100 timesteps. The smaller you make this number the more output will
+%% be generated! See Section \ref{sec:Movies} for a discussion on the
+%% generation of movies. This feature is not used at the time of meshing
+%% but is relevant for the solver.
+%% \item [{\texttt{CREATE\_SHAKEMAP}}] Set this flag to \texttt{.true.} to
+%% create a ShakeMap\textregistered, i.e., a peak ground velocity map
+%% of the maximum absolute value of the two horizontal components of the velocity vector.
+%% \item [{\texttt{SAVE\_DISPLACEMENT}}] Set this flag to \texttt{.true.}
+%% if you want to save the displacement instead of velocity for the movie
+%% frames.
+%% \item [{\texttt{USE\_HIGHRES\_FOR\_MOVIES}}] Set this flag to \texttt{.true.}
+%% if you want to save the values at all the NGLL grid points for the
+%% movie frames.
+\item [{\texttt{CREATE\_ABAQUS\_FILES}}] Set this flag to \texttt{.true.} to save Abaqus FEA \url{www.simulia.com}
+mesh files for subsequent viewing. Turning the flag on generates files in the \texttt{LOCAL\_PATH} directory.
+See Section~\ref{sec:Mesh-graphics} for a discussion of mesh viewing features.
+\item [{\texttt{CREATE\_DX\_FILES}}] Set this flag to \texttt{.true.} to save OpenDX \url{www.opendx.org}
+mesh files for subsequent viewing.
+
+%% \item [{\texttt{SAVE\_MESH\_FILES}}] Set this flag to \texttt{.true.} to
+%% save AVS \url{www.avs.com}, OpenDX \url{www.opendx.org}, or ParaView \url{www.paraview.org}
+%% mesh files for subsequent viewing. Turning the flag on generates large
+%% (distributed) files in the \texttt{LOCAL\_PATH} directory. See Section~\ref{sec:Mesh-graphics}
+%% for a discussion of mesh viewing features.
\item [{\texttt{LOCAL\_PATH}}] Directory in which the databases generated
by the mesher will be written. Generally one uses a directory on the
local disk of the compute nodes, although on some machines these databases
@@ -433,40 +459,56 @@
mesher finishes, you can log in to one of the compute nodes and view
the contents of the \texttt{LOCAL\_PATH} directory to see the (many)
files generated by the mesher.
-\item [{\texttt{NTSTEP\_BETWEEN\_OUTPUT\_INFO}}] This parameter specifies
-the interval at which basic information about a run is written to
-the file system (\texttt{timestamp{*}} files in the \texttt{OUTPUT\_FILES}
-directory). If you have access to a fast machine, set \texttt{NTSTEP\_BETWEEN\_OUTPUT\_INFO}
-to a relatively high value (e.g., at least 100, or even 1000 or more)
-to avoid writing output text files too often. This feature is not
-used at the time of meshing. One can set this parameter to a larger
-value than the number of time steps to avoid writing output during
-the run.
-\item [{\texttt{NTSTEP\_BETWEEN\_OUTPUT\_SEISMOS}}] This parameter specifies
-the interval at which synthetic seismograms are written in the \texttt{LOCAL\_PATH}
-directory. If a run crashes, you may still find usable (but shorter
-than requested) seismograms in this directory. On a fast machine set
-\texttt{NTSTEP\_BETWEEN\_OUTPUT\_SEISMOS} to a relatively high value
-to avoid writing to the seismograms too often. This feature is not
-used at the time of meshing.
-\item [{\texttt{PRINT\_SOURCE\_TIME\_FUNCTION}}] Turn this flag on to print
-information about the source time function in the file \texttt{OUTPUT\_FILES/plot\_source\_time\_function.txt}.
-This feature is not used at the time of meshing.
+\item [{\texttt{NMATERIALS}}] The number of different materials in your model. In the following lines, each material needs to be defined as :
+\begin{lyxcode}
+\texttt{material\_ID} \texttt{rho} \texttt{vp} \texttt{vs} \texttt{Q\_flag} \texttt{anisotropy\_flag} \texttt{domain\_ID}
+\end{lyxcode}
+where
+\begin{itemize}
+ \item \texttt{Q\_flag} : 0=no attenuation / standard \texttt{Q} attenutation value
+ \item \texttt{anisotropy\_flag} : 0=no anisotropy / 1,2,.. check with implementation in \texttt{aniso\_model.f90}
+ \item \texttt{domain\_id} : 1=acoustic / 2=elastic / 3=poroelastic
+\end{itemize}
+\item [{\texttt{NMATERIALS}}] The number of regions in the mesh.
+In the following lines, because the mesh is regular or 'almost regular', each region is defined as :
+\begin{lyxcode}
+ \texttt{XI\_begin} \texttt{XI\_end} \texttt{ETA\_begin} \texttt{ETA\_end} \texttt{material\_ID}
+\end{lyxcode}
+
+%% \item [{\texttt{NTSTEP\_BETWEEN\_OUTPUT\_INFO}}] This parameter specifies
+%% the interval at which basic information about a run is written to
+%% the file system (\texttt{timestamp{*}} files in the \texttt{OUTPUT\_FILES}
+%% directory). If you have access to a fast machine, set \texttt{NTSTEP\_BETWEEN\_OUTPUT\_INFO}
+%% to a relatively high value (e.g., at least 100, or even 1000 or more)
+%% to avoid writing output text files too often. This feature is not
+%% used at the time of meshing. One can set this parameter to a larger
+%% value than the number of time steps to avoid writing output during
+%% the run.
+%% \item [{\texttt{NTSTEP\_BETWEEN\_OUTPUT\_SEISMOS}}] This parameter specifies
+%% the interval at which synthetic seismograms are written in the \texttt{LOCAL\_PATH}
+%% directory. If a run crashes, you may still find usable (but shorter
+%% than requested) seismograms in this directory. On a fast machine set
+%% \texttt{NTSTEP\_BETWEEN\_OUTPUT\_SEISMOS} to a relatively high value
+%% to avoid writing to the seismograms too often. This feature is not
+%% used at the time of meshing.
+%% \item [{\texttt{PRINT\_SOURCE\_TIME\_FUNCTION}}] Turn this flag on to print
+%% information about the source time function in the file \texttt{OUTPUT\_FILES/plot\_source\_time\_function.txt}.
+%% This feature is not used at the time of meshing.
\end{description}
The topography of the model is defined as a set of elevation
values on a regular 2D grid. It is also posible to
define interfaces between the layers of the model in the same way.
-The file \texttt{meshfem3D/DATA/interfaces.dat} contains the settings of the topography grid
+The file defined in \texttt{INTERFACES\_FILE} contains the settings of the topography grid
and of the interfaces grids. The number
of interfaces, including the topography, needs to be set at the first line. Then, from the bottom
to the top of the model, you need to define the grids with several parameters :
number of points along $x$ and $y$, minimal $x$ and $y$ coordinates, spacing between points and the file
-where the elevation values are stored. At the end of this file, you simply need to set the
-number of spectral elements in the vertical direction for each layer.
+in which the elevation values are stored. At the end of this file, you simply need to set the
+number of spectral elements in the vertical direction for each layer.\\
-Finally, you need to provide a file that tells MPI what compute nodes
+Finally, depending on your system, you might need to provide a file that tells MPI what compute nodes
to use for the simulations. The file must have a number of entries
(one entry per line) at least equal to the number of processors needed
for the run. A sample file is provided in the file \texttt{mymachines}.
@@ -495,43 +537,44 @@
!~integer,~parameter~::~IMAIN~=~ISTANDARD\_OUTPUT
\end{lyxcode}
-Another file generated by the mesher is the header file \texttt{OUTPUT\_FILES/values\_from\_mesher.h}.
-This file specifies a number of constants and flags needed by the
-solver. These values are passed statically to the solver for reasons
-of speed. Some useful statistics about the mesh are also provided
-in this file.
+%% Another file generated by the mesher is the header file \texttt{OUTPUT\_FILES/values\_from\_mesher.h}.
+%% This file specifies a number of constants and flags needed by the
+%% solver. These values are passed statically to the solver for reasons
+%% of speed. Some useful statistics about the mesh are also provided
+%% in this file.
-For a given model, set of nodes, and set of parameters in \texttt{Par\_file},
-one only needs to run the mesher once and for all, even if one wants
-to run several simulations with different sources and/or receivers
-(the source and receiver information is used in the solver only).
+%% For a given model, set of nodes, and set of parameters in \texttt{Par\_file},
+%% one only needs to run the mesher once and for all, even if one wants
+%% to run several simulations with different sources and/or receivers
+%% (the source and receiver information is used in the solver only).
-\section{Checking the MPI Buffers (Optional)}
+%% \section{Checking the MPI Buffers (Optional)}
-The mesher writes MPI communication tables in the \texttt{OUTPUT\_FILES}
-subdirectory in the files \texttt{addressing.txt}, \texttt{list\_messages\_corners.txt}
-and \texttt{list\_messages\_faces.txt}, and MPI communication buffers
-to the local disks. Use the four serial codes
+%% The mesher writes MPI communication tables in the \texttt{OUTPUT\_FILES}
+%% subdirectory in the files \texttt{addressing.txt}, \texttt{list\_messages\_corners.txt}
+%% and \texttt{list\_messages\_faces.txt}, and MPI communication buffers
+%% to the local disks. Use the four serial codes
-\begin{lyxcode}
-check\_buffers\_2D.f90
+%% \begin{lyxcode}
+%% check\_buffers\_2D.f90
-check\_buffers\_1D.f90
-\end{lyxcode}
-to check that all the MPI buffers created by the mesher have been
-generated correctly. For example, typing `\texttt{make check\_buffers\_2D}'
-and then `\texttt{xcheck\_buffers\_2D}' checks the communication buffers
-between faces common to the mesh slices.
+%% check\_buffers\_1D.f90
+%% \end{lyxcode}
+%% to check that all the MPI buffers created by the mesher have been
+%% generated correctly. For example, typing `\texttt{make check\_buffers\_2D}'
+%% and then `\texttt{xcheck\_buffers\_2D}' checks the communication buffers
+%% between faces common to the mesh slices.
-\begin{quote}
-Please note that running these codes is optional because no information
-needed by the solver is generated.
-\end{quote}
+%% \begin{quote}
+%% Please note that running these codes is optional because no information
+%% needed by the solver is generated.
+%% \end{quote}
-\section{\label{sec:quality}Checking the Mesh Quality (Optional)}
+%%\section{\label{sec:quality}Checking the Mesh Quality (Optional)}
-The quality of the mesh may be inspected based upon the serial code
+\newpage{}
+The quality of the mesh may be inspected more precisely based upon the serial code
\texttt{check\_mesh\_quality\_AVS\_DX.f90}. Type
\begin{lyxcode}
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