[cig-commits] r16334 - seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL
bozdag at geodynamics.org
bozdag at geodynamics.org
Wed Feb 24 15:26:26 PST 2010
Author: bozdag
Date: 2010-02-24 15:26:26 -0800 (Wed, 24 Feb 2010)
New Revision: 16334
Modified:
seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/bibliography.bib
seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.pdf
seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex
Log:
Updated the manual and the BibTex file
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/bibliography.bib
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/bibliography.bib 2010-02-24 20:49:42 UTC (rev 16333)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/bibliography.bib 2010-02-24 23:26:26 UTC (rev 16334)
@@ -3824,6 +3824,16 @@
address = {Amsterdam}
}
+ at ARTICLE{EUCrust07,
+ author = {M. Tesauro and M. K. Kaban and S. A. P. L. Cloetingh},
+ title = {EuCrust-07: A new reference model for the European crust},
+ journal = grl,
+ year = {2008},
+ volume = {35},
+ pages = {L05313},
+ doi = {10.1029/2007GL032244}
+}
+
@BOOK{Euv94,
title = {R\'esolution num\'erique des \'equations aux d\'eriv\'ees partielles
- Diff\'erences finies, \'el\'ements finis, probl\`emes en domaine
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.pdf
===================================================================
(Binary files differ)
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex 2010-02-24 20:49:42 UTC (rev 16333)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex 2010-02-24 23:26:26 UTC (rev 16334)
@@ -1,4 +1,4 @@
-%% LyX 1.5.1 created this file. For more info, see http://www.lyx.org/.
+%% LyX 1.5.1 created this file. For more info, see www.lyx.org/.
\documentclass[oneside,english]{book}
\usepackage[T1]{fontenc}
@@ -97,7 +97,7 @@
\textbf{User Manual}}
-\author{$\copyright$ California Institute of Technology (USA) and\\
+\author{$\copyright$ California Institute of Technology / Princeton University (USA) and\\
University of Pau / CNRS / INRIA (France)\\
Version 5.0.0 `Tiger'}
@@ -452,6 +452,10 @@
\item [{\texttt{3D\_attenuation}}] See Chapter~\ref{cha:-Changing-the}
for a discussion on how to specify your own 3D attenuation model.
\end{description}
+\item [{\textmd{NOTE:}}]~\\
+When a 3D mantle model is chosen in \texttt{Par\_file}, the simulations are performed together with 3D crustal model Crust2.0. Alternatively, Crust2.0 can be combined with a higher resolution European crustal model EUCrust07 \citep{EUCrust07}. This can be done by setting the crustal type to \texttt{ICRUST\_CRUSTMAPS} in the \texttt{constant.h} file.
+It is also possible to run simulations using a 3D mantle model with a 1D crustal model on top. This can be done by setting the model in \texttt{Par\_file} to \texttt{<3D mantle>\_1Dcrust}, e.g., \texttt{s20rts\_1Dcrust, s362ani\_1Dcrust}, etc. In this case, 1D crustal model will be the one that is used in the 3D mantle model as a reference model (e.g., transversely isotropic PREM for s20rts, REF for s362ani, etc.).
+
\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
@@ -557,7 +561,7 @@
and \texttt{OUTPUT\_SEI-}~\\
\texttt{SMOS\_SAC\_BINARY}. One can choose any combination of these
parameters (details on the formats follow in the description of each
-parameter). SAC \url{www.llnl.gov/sac} is a signal-processing software
+parameter). SAC \url{www.iris.edu/software/sac/} is a signal-processing software
package. 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
@@ -574,15 +578,12 @@
if you want to have the synthetic seismograms written in alphanumeric
(human readable) SAC format, which includes header information on
the source and receiver parameters (e.g., source/receiver coordinates,
-station name, etc.). For details on the format, please check the SAC \url{www.llnl.gov/sac}
-webpage. Files will be named with extension \texttt{.sacan}.
+station name, etc., see Appendix~\ref{cha:SAC-headers}). For details on the format, please check the SAC webpage \url{www.iris.edu/software/sac/}. Files will be named with extension \texttt{.sacan}.
\item [{\texttt{OUTPUT\_SEISMOS\_SAC\_BINARY}}] Set this flag to \texttt{.true.}
if you want to have the synthetic seismograms written in binary SAC
format. The header information included is the same as for the alphanumeric
-SAC format. Using this format requires the least disk space, which
-may be particulary important if you have a large number of stations.
-For details on the binary format please also check the SAC \url{www.llnl.gov/sac}
-webpage. Files will be named with extension \texttt{.sac}.
+SAC format (see Appendix~\ref{cha:SAC-headers}). Using this format requires the least disk space, which may be particulary important if you have a large number of stations.
+For details on the binary format please also check the SAC webpage \url{www.iris.edu/software/sac/} and Appendix~\ref{cha:SAC-headers}. Files will be named with extension \texttt{.sac}.
\item [{\texttt{ROTATE\_SEISMOGRAMS\_RT}}] Set this flag to \texttt{.true.}
if you want to have radial (R) and transverse (T) horizontal components
of the synthetic seismograms (default is \texttt{.false.} $\rightarrow$
@@ -1006,34 +1007,6 @@
Please note that running these codes is optional because no information
needed by the solver is generated.
-
-\section{\label{sec:Checking-the-Mesh}Checking the Mesh Quality (Optional)}
-
-The quality of the mesh may be analyzed based on the serial code \texttt{check\_mesh\_quality\_AVS\_DX.f90}.
-Type `\texttt{make check\_mesh\_quality\_AVS\_DX}' and then use `\texttt{xcheck\_mesh\_quality\_AVS\_DX}'
-to generate an AVS output file (\texttt{AVS\_meshquality.inp} in AVS
-UCD format) or an OpenDX output file (\texttt{DX\_meshquality.dx})
-that can be used to investigate mesh quality, for example, skewness
-of elements and a Gnuplot histogram (\texttt{mesh\_quality}~\\
-\texttt{\_histogram.txt}) that can be plotted with gnuplot (type `\texttt{gnuplot
-plot\_mesh\_quality\_histogram.gnu}'). The histogram is also printed
-to the screen. If you want to start designing your own meshes, this
-tool is useful for viewing your creations. Your goal should then be
-to obtain meshes with elements that are as close as possible to regular
-hexahedra, i.e., the mesh should contain no very elongated or skewed
-elements.
-
-Note that using this code is helpful mostly when running local or
-regional simulations using SPECFEM3D, because in that case designing
-your own mesh may be useful in some cases. On the contrary, when meshing
-the global Earth using SPECFEM3D\_GLOBE, the default mesh provided,
-which has already been optimized to maximize mesh quality, should
-be sufficient.
-
-Also note that running this code is optional because no information
-needed by the solver is generated.
-
-
\chapter{\label{cha:Running-the-Solver}Running the Solver \texttt{xspecfem3D}}
Now that you have successfully run the mesher, you are ready to compile
@@ -1072,7 +1045,7 @@
the mesher and the solver.
For any particular earthquake, the \texttt{CMTSOLUTION} file that
-represents the point source may be obtained directly from the Harvard Centroid-Moment Tensor (CMT) web page \url{www.seismology.harvard.edu}.
+represents the point source may be obtained directly from the Harvard Centroid-Moment Tensor (CMT) web page \url{www.globalcmt.org}.
It looks like this:
\begin{lyxcode}
@@ -1096,10 +1069,6 @@
The \texttt{CMTSOLUTION} should be edited in the following way:
\begin{itemize}
-\item Set the \texttt{time shift} parameter equal to $0.0$ (the solver
-will not run otherwise.) The time shift parameter would simply apply
-an overall time shift to the synthetics, something that can be done
-in the post-processing (see Section \ref{sec:Process-data-and-syn}).
\item For point-source simulations (see finite sources, page \pageref{To-simulate-a})
we recommend setting the source half-duration parameter \texttt{half
duration} equal to zero, which corresponds to simulating a step source-time
@@ -1119,7 +1088,7 @@
with the \texttt{-h} flag, or the serial code \texttt{convolve\_source\_timefunction.f90}
and the script \texttt{UTILS/convolve\_source\_timefunction.csh} for
this purpose, or alternatively use signal-processing software packages
-such as SAC \url{www.llnl.gov/sac}. Type
+such as SAC \url{www.iris.edu/software/sac/}. Type
\begin{lyxcode}
make~convolve\_source\_timefunction
@@ -1163,6 +1132,8 @@
file adheres to the Harvard CMT conventions (see Appendix~\ref{cha:Reference-Frame-Convention}).
Note that the first line in the \texttt{CMTSOLUTION} file is the Preliminary Determination of Earthquakes (PDE) solution performed by the USGS NEIC, which is used as a seed for the Harvard CMT inversion. The PDE solution is based upon P waves and often gives the hypocenter of the earthquake, i.e., the rupture initiation point, whereas the CMT solution gives the `centroid location', which is the location with dominant moment release. The PDE solution is not used by our software package but must be present anyway in the first line of the file.
+In the current version of the code, the solver can run with a non-zero \texttt{time shift} in the \texttt{CMTSOLUTION} file. Thus one does not need to set \texttt{time shift} to zero as it was the case for previous versions of the code. \texttt{time shift} is only used for writing centroid time in the SAC headers (see Appendix~\ref{cha:SAC-headers}). CMT time is obtained by adding \texttt{time shift} to the PDE time given in the first line in the \texttt{CMTSOLUTION} file. Therefore it is recommended not to modify \texttt{time shift} to have the correct timing information in the SAC headers without any post-processing of seismograms.
+
\label{To-simulate-a}To simulate a kinematic rupture, i.e., a finite-source
event, represented in terms of $N_{\mathrm{sources}}$ point sources,
provide a \texttt{CMTSOLUTION} file that has $N_{\mathrm{sources}}$
@@ -1170,12 +1141,12 @@
\texttt{CMTSOLUTION} files to a single \texttt{CMTSOLUTION} file).
At least one entry (not necessarily the first) must have a zero \texttt{time
shift}, and all the other entries must have non-negative \texttt{time
-shift}. Each subevent can have its own half duration, latitude, longitude,
+shift}. If none of the entries has a zero \texttt{time shift} in the \texttt{CMTSOLUTION} file, the smallest \texttt{time shift} is subtracted from all sources to initiate the simulation. Each subevent can have its own half duration, latitude, longitude,
depth, and moment tensor (effectively, the local moment-density tensor).
Note that the zero in the synthetics does NOT represent the hypocentral
time or centroid time in general, but the timing of the \textit{center}
-of the source triangle with zero \texttt{time shift} (Fig~\ref{fig:source_timing}).
+of the source triangle with zero \texttt{time shift} (Fig~\ref{fig:source_timing}).
Although it is convenient to think of each source as a triangle, in
the simulation they are actually Gaussians (as they have better frequency
@@ -1431,11 +1402,7 @@
of elements needs to be adjusted as well to maintain spectral elements
that are as cube-like as possible. The code attempts to do this, but
be sure to view the mesh with your favorite graphics package to make
-sure that the element are well behaved. We also recommend that you
-use the serial code \texttt{check\_mesh\_quality\_AVS\_DX.f90} to
-check the quality of the mesh (see Section~\ref{sec:Checking-the-Mesh}).
-Remember: a high-quality mesh is paramount for accurate simulations.
-In addition to a reorganization of the radial distribution of elements,
+sure that the element are well behaved. Remember: a high-quality mesh is paramount for accurate simulations. In addition to a reorganization of the radial distribution of elements,
the time stepping and period range in which the attenuation is applied
is automatically determined. The minimum and maximum periods for attenuation
are:
@@ -1749,7 +1716,7 @@
chunks, the source and receiver location, etc. Use the AVS UCD files
\texttt{AVS\_continent\_boundaries.inp} and \texttt{AVS\_plate\_boundaries.inp}
or the OpenDX files \texttt{DX\_continent\_boundaries.dx} and \texttt{DX\_plate\_boundaries.dx}
-(that can be created using Perl scripts located in \texttt{DATA/UTILS/opendx\_AVS})
+(that can be created using Perl scripts located in \texttt{UTILS/Visualization/opendx\_AVS})
for reference.
@@ -1890,14 +1857,15 @@
circle path, it is sufficient to collect only the slices that are
along or close to the great circle path.
-A Perl script \texttt{UTILS/Paraview/global\_slice\_number.pl} can
+A Perl script \texttt{UTILS/Visualization/Paraview/global\_slice\_number.pl} can
help to figure out the slice numbers that lie along the great circle
path (both the minor and major arcs), as well as the slice numbers
required to produce a full picture of the inner core if your kernel
also illuminates the inner core.
\begin{enumerate}
-\item You need to first compile the utility programs provided in the \texttt{UTILS/Paraview/global\_slice\_util
+\item You need to first compile the utility programs provided in the \texttt{UTILS/Visualization/Paraview/}~\\
+\texttt{global\_slice\_util
}directory. Then copy the \texttt{CMTSOLUTION} file, \texttt{STATIONS\_ADJOINT},
and \texttt{Par\_file}, and run:
@@ -2000,7 +1968,8 @@
mesh2vtu.pl~-i~file.mesh~-o~file.vtu
\end{lyxcode}
\item Notice that this Perl script uses a program \texttt{mesh2vtu} in the
-\texttt{UTILS/Parview/mesh2vtu} directory, which further uses the
+\texttt{UTILS/Visualization/Paraview/}~\\
+\texttt{mesh2vtu} directory, which further uses the
VTK \url{www.vtk.org} run-time library for its execution. Therefore,
make sure you have them properly set in the script.
\end{enumerate}
@@ -2096,7 +2065,7 @@
main scripts are \texttt{\small run\_lsf.bash}, which compiles the
Fortran code and submits the job to the scheduler, and \texttt{\small go\_mesher\_solver\_lsf}~\\
\texttt{\small .bash}, which contains the instructions that make up
-the job itself. These scripts can be found in \texttt{\small UTILS/}
+the job itself. These scripts can be found in \texttt{\small UTILS/Cluster/lsf}
directory and can straightforwardly be modified and adapted to meet
more specific running needs.
@@ -2174,7 +2143,7 @@
\item The script then creates a list of the nodes allocated to this job
by echoing the value of a dynamically set environment variable \texttt{LSB\_MCPU\_HOSTS}
and parsing the output into a one-column list using the Perl script
-\texttt{UTILS/remap\_lsf\_machines.pl}. It then creates a set of scratch
+\texttt{UTILS/Cluster/lsf/remap\_lsf\_machines.pl}. It then creates a set of scratch
directories on these nodes (\texttt{\small /scratch/}~\\
\texttt{\small \$USER/DATABASES\_MPI}) to be used as the \texttt{LOCAL\_PATH}
for temporary storage of the database files. The scratch directories
@@ -2233,7 +2202,7 @@
For kernel simulations, you can use the sample run scripts \texttt{run\_lsf.kernel}
and \texttt{go\_mesher\_solver\_globe}~\\
-\texttt{.kernel} provided in \texttt{UTILS} directory, and modify
+\texttt{.kernel} provided in \texttt{UTILS/Cluster} directory, and modify
the command-line arguments of \texttt{xcut\_velocity} in \texttt{go\_mesher\_}~\\
\texttt{solver\_globe.kernel }according to the start and end time
of the specific portion of the forward seismograms you are interested
@@ -2615,7 +2584,7 @@
scratch disk for the next simulation. This is especially important
in the case of 1- or 2-chunk kernel simulation, where very large files
are generated for the absorbing boundaries to help with the reconstruction
-of the regular forward wavefield. A sample script is provided in \texttt{UTILS/}:
+of the regular forward wavefield. A sample script is provided in \texttt{UTILS/Cluster/lsf}:
\begin{lyxcode}
cleanbase.pl~machines
@@ -2770,7 +2739,7 @@
Hj\"orleifsd\'ottir, Sue Kientz, Dimitri Komatitsch, Qinya Liu, Alessia
Maggi, David Mich\'ea, Brian Savage, Anne Sieminski, Carl Tape, and
Jeroen Tromp. The manual's cover graphic was created by Santiago Lombeyda
-from Caltech's Center for Advanced Computing Research (CACR) \url{http://www.cacr.caltech.edu/}.
+from Caltech's Center for Advanced Computing Research (CACR) \url{www.cacr.caltech.edu/}.
Older versions of the code were initially developed by Dimitri Komatitsch at Institut de Physique du Globe (France)
and then by Dimitri Komatitsch and Jeroen Tromp at Harvard University (USA).
@@ -2782,11 +2751,11 @@
Main authors: Dimitri Komatitsch and Jeroen Tromp
-Seismological Laboratory, California Institute of Technology, USA,
+Seismological Laboratory, California Institute of Technology / Princeton University, USA,
and University of Pau / CNRS / INRIA, France
-$\copyright$ California Institute of Technology and University of Pau / CNRS
-/ INRIA, February 2010
+$\copyright$ California Institute of Technology / Princeton University and University of Pau / CNRS
+/ INRIA, March 2010
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published
@@ -2952,7 +2921,17 @@
contains the normal-mode and SEM seismograms, and the parameters (\texttt{STATIONS},
\texttt{CMTSOLUTION} and \texttt{Par\_file}) for the SEM simulations.
+\chapter{\label{cha:SAC-headers}SAC Headers}
+Most information about the simulations (i.e., event/station information, sampling rate, etc.) are written in the headers of the seismograms in SAC format. The list of headers and their explanations may be found in Figure \ref{fig:SAC-headers}. Please check the SAC webpages \url{www.iris.edu/software/sac/} for further information. Please note that the reference time KZTIME is the centroid time ($t_\text{CMT}=t_\text{PDE}+\texttt{time shift}$) which corresponds to zero time in the synthetics. For kinematic rupture simulations, KZTIME equals to the CMT time of the source having the minimum time-shift in the \texttt{CMTSOLUTION} file, and coordinates, depth and half-duration of the event are not provided in the headers.
+
+\begin{figure}[ht]
+\noindent \begin{centering}
+\includegraphics[scale=0.8]{figures/headers_sem_explained.pdf}\caption{\label{fig:SAC-headers}List of SAC headers and their explanations for a sample seismogram.}
+
+\par\end{centering}
+\end{figure}
+
\chapter{\label{cha:License}License}
\textbf{GNU GENERAL PUBLIC LICENSE Version 2, June 1991. Copyright
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