[cig-commits] r13923 - seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL
sue at geodynamics.org
sue at geodynamics.org
Thu Jan 22 14:27:32 PST 2009
Author: sue
Date: 2009-01-22 14:27:32 -0800 (Thu, 22 Jan 2009)
New Revision: 13923
Added:
seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex
Removed:
seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.lyx
Log:
added tex version of manual; removed lyx version
Deleted: seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.lyx
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.lyx 2009-01-22 22:15:26 UTC (rev 13922)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.lyx 2009-01-22 22:27:32 UTC (rev 13923)
@@ -1,38537 +0,0 @@
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-SPECFEM3D_GLOBE
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-\newline
-
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-User Manual
-\end_layout
-
-\begin_layout Author
-© California Institute of Technology (U.S.) and
-\newline
-University of Pau / CNRS /
- INRIA (France)
-\newline
-Version 4.0
-\end_layout
-
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-
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-\begin_layout Chapter
-Introduction
-\end_layout
-
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-
-\shape italic
-\begin_inset Quotes eld
-\end_inset
-
-Petaflops for your seismograms
-\begin_inset Quotes erd
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The software package SPECFEM3D_GLOBE simulates three-dimensional global
- and regional seismic wave propagation based upon the spectral-element method
- (SEM).
- Effects due to lateral variations in compressional-wave speed, shear-wave
- speed, density, a 3D crustal model, ellipticity, topography and bathymetry,
- the oceans, rotation, and self-gravitation are included.
- For a detailed introduction to the SEM as applied to global and regional
- seismic wave propagation, please consult
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoVi98,KoTr99,Ch00,KoTr02a,KoTr02b,KoRiTr02,ChCaVi03,CaChViMo03,ChVa04}
-\end_layout
-
-\end_inset
-
-.
- If you use 3D mantle model S20RTS, please cite
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{RiVaWo99}
-\end_layout
-
-\end_inset
-
-.
- The package can accommodate full 21-parameter anisotropy
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{ChTr07}
-\end_layout
-
-\end_inset
-
- as well as lateral variations in attenuation
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{SavWiTr05}
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-
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-.
- Adjoint capabilities and finite-frequency kernel simulations are also included
-
-\begin_inset ERT
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-
-
-\backslash
-citep{LiTr06,LiTr08}
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-All SPECFEM3D_GLOBE software is written in Fortran90 with full portability
- in mind, and conforms strictly to the Fortran95 standard.
- It uses no obsolete or obsolescent features of Fortran77.
- The package uses parallel programming based upon the Message Passing Interface
- (MPI)
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{GrLuSk94,Pac97}
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-SPECFEM3D won the Gordon Bell award for best performance at the SuperComputing\InsetSpace ~
-20
-03 conference in Phoenix, Arizona (U.S.) by running at 5 teraflops (sustained)
- on 1944 processors of the Japanese Earth Simulator using 14.6 billion degrees
- of freedom stored in 2.5 terabytes of memory; see
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
-
-\backslash
-cite{KoTsChTr03}
-\end_layout
-
-\end_inset
-
- and the
-\begin_inset LatexCommand htmlurl
-name "Gordon Bell Awards News Release"
-target "www.sc-conference.org/sc2003/nr_finalaward.html "
-
-\end_inset
-
- for details.
-\end_layout
-
-\begin_layout Section
-Citation
-\end_layout
-
-\begin_layout Standard
-If you use SPECFEM3D_GLOBE for your own research, please cite at least one
- of the following articles:
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-cite {KoRiTr02,KoTr02a,KoTr02b,KoTr99}
-\end_layout
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- or
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-cite{KoVi98}
-\end_layout
-
-\end_inset
-
-.
- The corresponding BibTeX entries may be found in file
-\family typewriter
-USER_MANUAL/bibliography.bib
-\family default
- or in comments at the beginning of file
-\family typewriter
-specfem3D.f90
-\family default
-.
-
-\end_layout
-
-\begin_layout Section
-Support
-\end_layout
-
-\begin_layout Standard
-This material is based upon work supported by the U.S.
- National Science Foundation under Grants No.
- EAR-0406751 and EAR-0711177, by the French CNRS, French INRIA Sud-Ouest
- MAGIQUE-3D, French ANR NUMASIS under Grant No.
- ANR-05-CIGC-002, and European FP6 Marie Curie International Reintegration
- Grant No.
- MIRG-CT-2005-017461.
- Any opinions, findings, and conclusions or recommendations expressed in
- this material are those of the authors and do not necessarily reflect the
- views of the U.S.
- National Science Foundation, CNRS, INRIA, ANR or the European Marie Curie
- program.
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Getting-Started"
-
-\end_inset
-
-Getting Started
-\end_layout
-
-\begin_layout Standard
-The SPECFEM3D_GLOBE software package comes in a gzipped tar ball.
- In the directory in which you want to install the package, type
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-tar -zxvf SPECFEM3D_GLOBE_V4.0.0.tar.gz
-\end_layout
-
-\begin_layout Standard
-The directory
-\family typewriter
-SPECFEM3D_GLOBE_V4.0.0
-\family default
- will then contain the source code.
-\end_layout
-
-\begin_layout Standard
-To configure the software for your system, run the
-\family typewriter
-configure
-\family default
- shell script.
- This script will attempt to guess the appropriate configuration values
- for your system.
- However, at a minimum, it is recommended that you explicitly specify the
- appropriate command names for your Fortran90 compiler and MPI package:
-\end_layout
-
-\begin_layout LyX-Code
-./configure FC=ifort MPIFC=mpif90
-\end_layout
-
-\begin_layout Standard
-A summary of the most important configuration variables follows.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-FC
-\family default
- Fortran90 compiler command name.
- By default,
-\family typewriter
-configure
-\family default
- will execute the command names of various well-known Fortran compilers
- in succession, picking the first one it finds that works.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-MPIFC
-\family default
- MPI Fortran90 command name.
- The default is
-\family typewriter
-mpif90
-\family default
-.
- This must correspond to the same underlying compiler specified by
-\family typewriter
-FC
-\family default
-; otherwise, you will encounter compilation or link errors when you attempt
- to build the code.
- If you are unsure about this, it is usually safe to set both
-\family typewriter
-FC
-\family default
- and
-\family typewriter
-MPIFC
-\family default
- to the MPI compiler command for your system:
-\end_layout
-
-\begin_layout LyX-Code
-./configure FC=mpif90 MPIFC=mpif90
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-FLAGS_CHECK
-\family default
- Compiler flags for non-critical subroutines.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-FLAGS_NO_CHECK
-\family default
- Compiler flags for creating fast, production-run code for critical subroutines.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-LOCAL_PATH_IS_ALSO_GLOBAL
-\family default
- Set to
-\family typewriter
-.false.
-
-\family default
- on most cluster applications.
- For reasons of speed, the (parallel) mesher typically writes a (parallel)
- database for the solver on the local disks of the compute nodes.
- Some systems have no local disks (e.g., BlueGene or the Earth Simulator)
- and other systems have a fast parallel file system, in which case this
- variable should be set to
-\family typewriter
-.true.
-\family default
-.
- Note that this flag is not used by the mesher or the solver; it is only
- used for some of the post-processing.
-\end_layout
-
-\begin_layout Standard
-In addition to reading configuration variables,
-\family typewriter
-configure
-\family default
- accepts the following options:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
---enable-double-precision
-\family default
- The package can run either in single or in double precision.
- The default is single precision mode because this requires exactly half
- as much memory.
- To specify double precision mode, simply provide
-\family typewriter
---enable-double-precision
-\family default
- as a command-line argument to
-\family typewriter
-configure
-\family default
-.
- On a new system, it is definitely worth experimenting with single versus
- double precision simulations to determine which is faster.
- Note that on many current processors (e.g., Intel, AMD, IBM Power), single
- precision calculations are often significantly faster; the difference can
- typically be 10% to 25%.
- It is therefore worth trying single precision if you can.
- We recommend running the same calculation once in single precision and
- in double precision on your system and comparing the seismograms.
- If they are identical, you should probably select single precision for
- your future runs.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
---help
-\family default
- Directs
-\family typewriter
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-\family default
- to print a usage screen which provides a short description of all configuration
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- Note that the options relating to installation directories (e.g.,
-\family typewriter
---prefix
-\family default
-) do not apply to SPECFEM3D_GLOBE.
-\end_layout
-
-\begin_layout Standard
-The
-\family typewriter
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-\family default
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- Upon successful completion, it generates the files
-\family typewriter
-Makefile
-\family default
-,
-\family typewriter
-constants.h
-\family default
-, and
-\family typewriter
-precision.h
-\family default
- in the working directory.
-\end_layout
-
-\begin_layout Description
-Note: If the
-\family typewriter
-configure
-\family default
- script fails, and you don't know what went wrong, examine the log file
-
-\family typewriter
-config.log
-\family default
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-\family typewriter
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-\family default
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-\end_layout
-
-\begin_layout Standard
-The
-\family typewriter
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-\family default
- script automatically runs the script
-\family typewriter
-flags.guess
-\family default
-.
- This helper script contains a number of suggested flags for various compilers;
- e.g., Portland, Intel, Absoft, NAG, Lahey, NEC, IBM and SGI.
- The software has run on a wide variety of compute platforms, e.g., various
- PC clusters and machines from Sun, SGI, IBM, Compaq, and NEC.
- The
-\family typewriter
-flags.guess
-\family default
- script attempts to guess which compiler you are using (based upon the compiler
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- The
-\family typewriter
-configure
-\family default
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-\family typewriter
-Makefile
-\family default
-.
- Note that
-\family typewriter
-flags.guess
-\family default
- may fail to identify your compiler; and in any event, the default flags
- chosen by
-\family typewriter
-flags.guess
-\family default
- are undoubtedly not optimal for your system.
- So, we encourage you to experiment with these flags (by editing the generated
-
-\family typewriter
-Makefile
-\family default
- by hand) and to solicit advice from your system administrator.
- Selecting the right compiler and compiler flags can make a tremendous differenc
-e in terms of performance.
- We welcome feedback on your experience with various compilers and flags.
-\end_layout
-
-\begin_layout Standard
-On SGI systems,
-\family typewriter
-flags.guess
-\family default
- automatically informs
-\family typewriter
-configure
-\family default
- to insert `
-\family typewriter
-`TRAP_FPE=OFF
-\family default
-'' into the generated
-\family typewriter
-Makefile
-\family default
- in order to turn underflow trapping off.
-\end_layout
-
-\begin_layout Standard
-Finally, before compiling, make sure that the subdirectories
-\family typewriter
-obj
-\family default
-,
-\family typewriter
-bak
-\family default
- and
-\family typewriter
-OUTPUT_FILES
-\family default
- exist within the directory with the source code (
-\family typewriter
-SPECFEM3D_GLOBE_V4.0.0
-\family default
-).
- The
-\family typewriter
-go_mesher
-\family default
- script discussed below automatically takes care of creating the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory.
-\end_layout
-
-\begin_layout Standard
-Note that if you run very large meshes on a relatively small number of processor
-s, the memory size needed on each processor might become greater than 2
- gigabytes, which is the upper limit for 32-bit addressing; in this case,
- on some compilers you may need to add
-\family typewriter
-``-mcmodel=medium
-\family default
-'' to the compiler options otherwise the compiler will display an error
- message.
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Running-the-Mesher"
-
-\end_inset
-
-Running the Mesher
-\family typewriter
-xmeshfem3D
-\end_layout
-
-\begin_layout Standard
-You are now ready to compile the mesher.
- In the directory with the source code, type `
-\family typewriter
-make meshfem3D
-\family default
-'.
- If all paths and flags have been set correctly, the mesher should now compile
- and produce the executable
-\family typewriter
-xmeshfem3D
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-Input for the mesher (and the solver) is provided through the parameter
- file
-\family typewriter
-Par_file
-\family default
-, which resides in the subdirectory
-\family typewriter
-DATA
-\family default
-.
- Before running the mesher, a number of parameters need to be set in the
-
-\family typewriter
-Par_file
-\family default
-.
- This requires a basic understanding of how the SEM is implemented, and
- we encourage you to read
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoVi98,KoTr99,Ch00,KoTr02a,KoTr02b,KoRiTr02,ChCaVi03,CaChViMo03}
-\end_layout
-
-\end_inset
-
- and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{ChVa04}
-\end_layout
-
-\end_inset
-
-.
- A detailed theoretical analysis of the dispersion and stability properties
- of the SEM is available in
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{DeSe07}
-\end_layout
-
-\end_inset
-
- and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{SeOl07}
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-In this chapter we will focus on simulations at the scale of the entire
- globe.
- Regional simulations will be addressed in Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
-.
- The spectral-element mesh for a SPECFEM3D_GLOBE simulation is based upon
- a mapping from the cube to the sphere called the
-\shape italic
-cubed sphere
-\shape default
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{Sad72,RoIaPa96}
-\end_layout
-
-\end_inset
-
-.
- This cubed-sphere mapping breaks the globe into 6\InsetSpace ~
-chunks, each of which
- is further subdivided in terms of
-\begin_inset Formula $n^{2}$
-\end_inset
-
- mesh slices, where
-\begin_inset Formula $n\ge1$
-\end_inset
-
- is a positive integer, for a total of
-\begin_inset Formula $6\times n^{2}$
-\end_inset
-
- slices (Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "figure:mpi_slices"
-
-\end_inset
-
-).
- Thus the minimum number of processors required for a global simulation
- is 6 (although it is theoretically possible to run more than one slice
- per processor).
-
-\begin_inset Float figure
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-sideways false
-status open
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-\begin_inset Tabular
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-
-\begin_layout Standard
-\begin_inset Graphics
- filename figures/mpi_slices.eps
- width 45text%
-
-\end_inset
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-
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-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" usebox="none">
-\begin_inset Text
-
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- filename figures/fullmesh_18.eps
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-
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-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Each of the 6\InsetSpace ~
-chunks that constitutes the cubed sphere is subdivided in terms
- of
-\begin_inset Formula $n^{2}$
-\end_inset
-
-\InsetSpace ~
-slices of elements, where
-\begin_inset Formula $n\ge1$
-\end_inset
-
- is a positive integer, for a total of
-\begin_inset Formula $6\times n^{2}$
-\end_inset
-
- slices (and therefore processors).
- The figure on the left shows a mesh that is divided in terms of
-\begin_inset Formula $6\times5^{2}=150$
-\end_inset
-
- slices as indicated by the various colors.
- In this cartoon, each slice contains
-\begin_inset Formula $5\times5=25$
-\end_inset
-
- spectral elements at the Earth's surface.
- The figure on the right shows a mesh that is divided over
-\begin_inset Formula $6\times18^{2}=1944$
-\end_inset
-
- processors as indicated by the various colors.
- Regional simulations can be accommodated by using only 1, 2 or 3 chunks
- of the cubed sphere.
- One-chunk simulations may involve a mesh with lateral dimensions smaller
- than\InsetSpace ~
-
-\begin_inset Formula $90^{\circ}$
-\end_inset
-
-, thereby accommodating smaller-scale simulations.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "figure:mpi_slices"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To run the mesher for a global simulation, the following parameters need
- to be set in the
-\family typewriter
-Par_file
-\family default
-:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-SIMULATION_TYPE
-\family default
- is set to 1 for forward simulations, 2 for adjoint simulations (see Section
-
-\begin_inset LatexCommand ref
-reference "sec:Adjoint-simulation-finite"
-
-\end_inset
-
-) and 3 for kernel simulations (see Section
-\begin_inset LatexCommand ref
-reference "sec:Finite-Frequency-Kernels"
-
-\end_inset
-
-).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-SAVE_FORWARD
-\family default
- is only set to
-\family typewriter
-.true.
-
-\family default
- for a forward simulation with the last frame of the simulation saved, as
- part of the finite-frequency kernel calculations (see Section
-\begin_inset LatexCommand ref
-reference "sec:Finite-Frequency-Kernels"
-
-\end_inset
-
-).
- For a regular forward simulation, leave
-\family typewriter
-SIMULATION_TYPE
-\family default
- and
-\family typewriter
-SAVE_FORWARD
-\family default
- at their default values.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NCHUNKS
-\family default
- must be set to 6 for global simulations.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ANGULAR_WIDTH_XI_IN_DEGREES
-\family default
- Not needed for a global simulation.
- (See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
- for regional simulations.)
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ANGULAR_WIDTH_ETA_IN_DEGREES
-\family default
- Not needed for a global simulation.
- (See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
- for regional simulations.)
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-CENTER_LATITUDE_IN_DEGREES
-\family default
- Not needed for a global simulation.
- (See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
- for regional simulations.)
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-CENTER_LONGITUDE_IN_DEGREES
-\family default
- Not needed for a global simulation.
- (See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
- for regional simulations.)
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-GAMMA_ROTATION_AZIMUTH
-\family default
- Not needed for a global simulation.
- (See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
- for regional simulations.)
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nexxi$
-\end_inset
-
- The number of spectral elements along one side of a chunk in the cubed
- sphere (see Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "figure:mpi_slices"
-
-\end_inset
-
-); this number
-\shape italic
-must
-\shape default
- be a multiple of 16 and 8\InsetSpace ~
-
-\begin_inset Formula $\times$
-\end_inset
-
-\InsetSpace ~
-a multiple of
-\begin_inset Formula $\nprocxi$
-\end_inset
-
- defined below.
- We do not recommend using
-\begin_inset Formula $\nexxi$
-\end_inset
-
- less than 64 because the curvature of the Earth cannot be honored if one
- uses too few elements, and distorted elements can lead to inaccurate and
- unstable simulations, i.e., smaller values of
-\begin_inset Formula $\nexxi$
-\end_inset
-
- are likely to result in spectral elements with a negative Jacobian, in
- which case the mesher will exit with an error message.
- Table\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "table:nex"
-
-\end_inset
-
- summarizes various suitable choices for
-\begin_inset Formula $\nexxi$
-\end_inset
-
- and the related values of
-\begin_inset Formula $\nprocxi$
-\end_inset
-
-.
- Based upon benchmarks against semi-analytical normal-mode synthetic seismograms
-,
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02a,KoTr02b}
-\end_layout
-
-\end_inset
-
- determined that a
-\begin_inset Formula $\nexxi=256$
-\end_inset
-
- run is accurate to a shortest period of roughly 17\InsetSpace ~
-s.
- Therefore, since accuracy is determined by the number of grid points per
- shortest wavelength, for any particular value of
-\begin_inset Formula $\nexxi$
-\end_inset
-
- the simulation will be accurate to a shortest period determined approximately
- by
-\begin_inset Formula \begin{equation}
-\mbox{shortest period (s)}\simeq(256/\nexxi)\times17.\label{eq:shortest_period}\end{equation}
-
-\end_inset
-
- The number of grid points in each orthogonal direction of the reference
- element, i.e., the number of Gauss-Lobatto-Legendre points, is determined
- by
-\family typewriter
-NGLLX
-\family default
- in the
-\family typewriter
-constants.h
-\family default
- file.
- In the globe we use
-\begin_inset Formula $\mbox{\texttt{NGLLX}}=5$
-\end_inset
-
-, for a total of
-\begin_inset Formula $5^{3}=125$
-\end_inset
-
- points per elements.
- We suggest not to change this value.
-
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nexeta$
-\end_inset
-
- For global simulations
-\begin_inset Formula $\nexeta$
-\end_inset
-
- must be set to the same value as
-\begin_inset Formula $\nexxi$
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nprocxi$
-\end_inset
-
- The number of processors or slices along one chunk of the cubed sphere
- (see Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "figure:mpi_slices"
-
-\end_inset
-
-); we must have
-\begin_inset Formula $\nexxi=8\times c\times\nprocxi$
-\end_inset
-
-, where
-\begin_inset Formula $c\ge1$
-\end_inset
-
- is a positive integer.
- See Table\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "table:nex"
-
-\end_inset
-
- for various suitable choices.
-
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nproceta$
-\end_inset
-
- For global simulations
-\begin_inset Formula $\nproceta$
-\end_inset
-
- must be set to the same value as
-\begin_inset Formula $\nprocxi$
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-MODEL
-\family default
- Must be set to one of the following:
-\end_layout
-
-\begin_layout Description
-
-\series medium
-1D\InsetSpace ~
-models\InsetSpace ~
-with\InsetSpace ~
-real\InsetSpace ~
-structure:
-\end_layout
-
-\begin_deeper
-\begin_layout Description
-
-\family typewriter
-1D_isotropic_prem
-\family default
- Isotropic version of the spherically symmetric Preliminary Reference Earth
- Model (PREM)
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{DzAn81}
-\end_layout
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-1D_transversely_isotropic_prem
-\family default
- Transversely isotropic version of PREM.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-1D_iasp91
-\family default
- Spherically symmetric isotropic IASP91 model
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{KeEn91}
-\end_layout
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-1D_1066a
-\family default
- Spherically symmetric earth model 1066A
-\begin_inset LatexCommand citep
-key "gilbertdziewonski1975"
-
-\end_inset
-
-.
- When
-\family typewriter
-\size small
-ATTENTUATION
-\family default
-\size default
- is on, it uses an unpublished 1D attenuation model from Scripps.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-1D_ak135
-\family default
- Spherically symmetric isotropic AK135 model
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{KeEnBu95}
-\end_layout
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-1
-\family default
-D_ref A recent 1D Earth model developed by
-\begin_inset LatexCommand citet
-key "KuDzEk06"
-
-\end_inset
-
-.
- This model is the 1D background model for the 3D models s362ani, s362wmani,
- s362ani_prem, and s29ea.
-\end_layout
-
-\end_deeper
-\begin_layout Standard
-For historical reasons and to provide benchmarks against normal-mode synthetics,
- the mesher accommodates versions of various 1D models with a single crustal
- layer with the properties of the original upper crust.
- These `one-crust' models are:
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-1D_isotropic_prem_onecrust
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-1D_transversely_isotropic_prem_onecrust
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-1D_iasp91_onecrust
-\family default
-,
-\family typewriter
-1D_1066a_onecrust
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-1D_ak135_onecrust
-\end_layout
-
-\begin_layout Description
-
-\series medium
-Fully\InsetSpace ~
-3D\InsetSpace ~
-models:
-\end_layout
-
-\begin_deeper
-\begin_layout Description
-
-\family typewriter
-transversely_isotropic_prem_plus_3D_crust_2.0
-\family default
- This model has CRUST2.0
-\begin_inset LatexCommand citep
-key "BaLaMa00"
-
-\end_inset
-
- on top of a transversely isotropic PREM.
- We first extrapolate PREM mantle velocity up to the surface, then overwrite
- the model with CRUST2.0
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-s20rts
-\family default
- By default, the code uses 3D mantle model S20RTS
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{RiVaWo99}
-\end_layout
-
-\end_inset
-
- and 3D crustal model Crust2.0
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{BaLaMa00}
-\end_layout
-
-\end_inset
-
-.
- Note that S20RTS uses transversely isotropic PREM as a background model,
- and that we use the PREM radial attenuation model when
-\family typewriter
-ATTENUATION
-\family default
- is incorporated.
- See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:-Changing-the"
-
-\end_inset
-
- for a discussion on how to change 3D models.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-s362ani
-\family default
-\color inherit
-A global shear-wave speed model developed by
-\begin_inset LatexCommand citet
-key "KuDzEk06"
-
-\end_inset
-
-.
- In this model, radial anisotropy is confined to the uppermost mantle.
- The model (and the corresponding mesh) incorporate tomography on the 650~km
- and 410~km discontinuities in the 1D reference model REF.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-s362wmani
-\family default
-\color inherit
-A version of S362ANI with anisotropy allowed throughout the mantle.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-s362ani_prem
-\family default
-\color inherit
-A version of S362ANI calculated using PREM as the 1D reference model.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-s29ea
-\family default
-\color inherit
-A global model with higher resolution in the upper mantle beneath Eurasia
- calculated using REF as the 1D reference model.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-3D_anisotropic
-\family default
- See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:-Changing-the"
-
-\end_inset
-
- for a discussion on how to specify your own 3D anisotropic model.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-3D_attenuation
-\family default
- See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:-Changing-the"
-
-\end_inset
-
- for a discussion on how to specify your own 3D attenuation model.
-
-\end_layout
-
-\end_deeper
-\begin_layout Description
-
-\family typewriter
-OCEANS
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
- if the effect of the oceans on seismic wave propagation should be incorporated
- based upon the approximate treatment discussed in
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02b}
-\end_layout
-
-\end_inset
-
-.
- 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\InsetSpace ~
-s and longer.
- At shorter periods the effect of water phases/reverberations is not taken
- into account, even when the flag is on.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ELLIPTICITY
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
- if the mesh should make the Earth model elliptical in shape according to
- Clairaut's equation
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{DaTr98}
-\end_layout
-
-\end_inset
-
-.
- This feature adds no cost to the simulation.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-TOPOGRAPHY
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
- if topography and bathymetry should be incorporated based upon model ETOPO5
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{Etopo5}
-\end_layout
-
-\end_inset
-
-.
- This feature adds no cost to the simulation.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-GRAVITY
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
- if self-gravitation should be incorporated in the Cowling approximation
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{KoTr02b,DaTr98}
-\end_layout
-
-\end_inset
-
-.
- Turning this feature on is relatively inexpensive, both from the perspective
- of memory requirements as well as in terms of computational speed.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ROTATION
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
- if the Coriolis effect should be incorporated.
- Turning this feature on is relatively cheap numerically.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ATTENUATION
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
- if attenuation should be incorporated.
- Turning this feature on increases the memory requirements significantly
- (roughly by a factor of\InsetSpace ~
-1.5), and is numerically fairly expensive.
- Of course for realistic simulations this flag should be turned on.
- See
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr99,KoTr02a}
-\end_layout
-
-\end_inset
-
- for a discussion on the implementation of attenuation based upon standard
- linear solids.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ABSORBING_CONDITIONS
-\family default
- Set to
-\family typewriter
-.false.
-
-\family default
- for global simulations.
- See Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Regional-Simulations"
-
-\end_inset
-
- for regional simulations.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-RECORD_LENGTH_IN_MINUTES
-\family default
- 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.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-MOVIE_SURFACE
-\family default
- Set to
-\family typewriter
-.false.
-\family default
-, 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
-\begin_inset LatexCommand ref
-reference "sec:Movies"
-
-\end_inset
-
- for a discussion on the generation of movies.
- This feature is not used at the time of meshing but is relevant for the
- solver.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-MOVIE_VOLUME
-\family default
- Set to
-\family typewriter
-.false.
-\family default
-, 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
-\begin_inset LatexCommand ref
-reference "sec:Movies"
-
-\end_inset
-
- for a discussion on the generation of movies.
- This feature is not used at the time of meshing but is relevant for the
- solver.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NTSTEP_BETWEEN_FRAMES
-\family default
- 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
-\begin_inset LatexCommand ref
-reference "sec:Movies"
-
-\end_inset
-
- for a discussion on the generation of movies.
- This feature is not used at the time of meshing but is relevant for the
- solver.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-HDUR_MOVIE
-\family default
- determines the half duration of the source time function for the movie
- simulations.
- When this parameter is set to be 0, a default half duration that corresponds
- to the accuracy of the simulation is provided.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-SAVE_MESH_FILES
-\family default
- Set this flag to
-\family typewriter
-.true
-\size small
-.
-
-\family default
-\size default
- to save
-\begin_inset LatexCommand htmlurl
-name "AVS"
-target "www.avs.com"
-
-\end_inset
-
-,
-\begin_inset LatexCommand htmlurl
-name "OpenDX"
-target "www.opendx.org"
-
-\end_inset
-
-, or
-\begin_inset LatexCommand htmlurl
-name "ParaView"
-target "www.paraview.org"
-
-\end_inset
-
- mesh files for subsequent viewing.
- Turning the flag on generates large (distributed) files in the
-\family typewriter
-LOCAL_PATH
-\family default
- directory.
- See Section\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Meshes"
-
-\end_inset
-
- for a discussion of mesh viewing features.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NUMBER_OF_RUNS
-\family default
- On machines with a run-time limit, for instance for a batch/queue system,
- a simulation may need to be completed in stages.
- This option allows you to select the number of stages in which the simulation
- will be completed (1, 2 or 3).
- Choose 1 for a run without restart files.
- This feature is not used at the time of meshing but is required for the
- solver.
- At the end of the first or second stage of a multi-stage simulation, large
- files are written to the file system to save the current state of the simulatio
-n.
- This state is read back from the file system at the beginning of the next
- stage of the multi-stage run.
- Reading and writing the states can be very time consuming depending on
- the nature of the network and the file system (in this case writing to
- the local file system, i.e., the disk on a node, is preferable).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NUMBER_OF_THIS_RUN
-\family default
- If you choose to perform the run in stages, you need to tell the solver
- what stage run to perform.
- This feature is not used at the time of meshing but is required for the
- solver.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-LOCAL_PATH
-\family default
- 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 are written on a parallel (global)
- file system (see also the earlier discussion of the
-\family typewriter
-LOCAL_PATH_IS_ALSO_GLOBAL
-\family default
- flag in Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Getting-Started"
-
-\end_inset
-
-).
- The mesher generates the necessary databases in parallel, one set for each
- of the
-\begin_inset Formula $6\times\nprocxi^{2}$
-\end_inset
-
- slices that constitutes the mesh (see Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "figure:mpi_slices"
-
-\end_inset
-
-).
- After the mesher finishes, you can log in to one of the compute nodes and
- view the contents of the
-\family typewriter
-LOCAL_PATH
-\family default
- directory to see the (many) files generated by the mesher.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NTSTEP_BETWEEN_OUTPUT_INFO
-\family default
- This parameter specifies the interval at which basic information about
- a run is written to the file system (
-\family typewriter
-timestamp*
-\family default
- files in the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory).
- If you have access to a fast machine, set
-\family typewriter
-NTSTEP_BETWEEN_OUTPUT_INFO
-\family default
- 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.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NTSTEP_BETWEEN_OUTPUT_SEISMOS
-\family default
- This parameter specifies the interval at which synthetic seismograms are
- written in the
-\family typewriter
-LOCAL_PATH
-\family default
- directory.
- The seismograms can be created in three different formats by setting the
- parameters
-\family typewriter
-OUTPUT_SEISMOS_ASCII_TEXT
-\family default
-,
-\family typewriter
-OUTPUT_SEISMOS_SAC_ALPHANUM
-\family default
- and
-\family typewriter
-OUTPUT_SEI-
-\newline
-SMOS_SAC_BINARY
-\family default
-.
- One can choose any combination of these parameters (details on the formats
- follow in the description of each parameter).
-
-\begin_inset LatexCommand htmlurl
-name "SAC"
-target "www.llnl.gov/sac"
-
-\end_inset
-
- 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
-\family typewriter
-NTSTEP_BETWEEN_OUTPUT_SEISMOS
-\family default
- to a relatively high value to avoid writing to the seismograms too often.
- This feature is not used at the time of meshing.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-NTSTEP_BETWEEN_READ_ADJSRC
-\family default
- The number of adjoint sources read in each time for an adjoint simulation.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-OUTPUT_SEISMOS_ASCII_TEXT
-\family default
- Set this flag to
-\family typewriter
-.true.
-
-\family default
- if you want to have the synthetic seismograms written in two-column ASCII
- format (the first column contains time in seconds and the second column
- the displacement in meters of the recorded signal, no header information).
- Files will be named with extension
-\family typewriter
-.ascii
-\family default
-.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-OUTPUT_SEISMOS_SAC_ALPHANUM
-\family default
- Set this flag to
-\family typewriter
-.true.
-
-\family default
- 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
-\begin_inset LatexCommand htmlurl
-name "SAC"
-target "www.llnl.gov/sac"
-
-\end_inset
-
- webpage.
- Files will be named with extension
-\family typewriter
-.sacan
-\family default
-.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-OUTPUT_SEISMOS_SAC_BINARY
-\family default
- Set this flag to
-\family typewriter
-.true.
-
-\family default
- 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
-\begin_inset LatexCommand htmlurl
-name "SAC"
-target "www.llnl.gov/sac"
-
-\end_inset
-
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-\family default
-.
-\end_layout
-
-\begin_layout Description
-
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-ROTATE_SEISMOGRAMS_RT
-\family default
- Set this flag to
-\family typewriter
-.true.
-
-\family default
- if you want to have radial (R) and transverse (T) horizontal components
- of the synthetic seismograms (default is
-\family typewriter
-.false.
-
-\family default
-
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-
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-
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- East (E) and North (N) components).
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-
-\begin_layout Description
-
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-WRITE_SEISMOGRAMS_BY_MASTER
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- Set this flag to
-\family typewriter
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-
-\family default
- if you want to have all the seismograms written by the master (no need
- to collect them on the nodes after the run).
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-SAVE_ALL_SEISMOS_IN_ONE_FILE
-\family default
- Set this flag to
-\family typewriter
-.true.
-
-\family default
- if you want to have all the seismograms saved in one large combined file
- instead of one file per seismogram to avoid overloading shared non-local
- file systems such as GPFS for instance.
-\end_layout
-
-\begin_layout Description
-
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-\family default
-Set this flag to
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-
-\family default
- if you want to use binary instead of ASCII for that large file (not used
- if SAVE_ALL_SEISMOS_IN _ONE_FILE = .false.)
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-
-\begin_layout Description
-
-\family typewriter
-RECEIVERS_CAN_BE_BURIED
-\family default
- This flag accommodates stations with instruments that are buried, i.e., the
- solver will calculate seismograms at the burial depth specified in the
-
-\family typewriter
-STATIONS
-\family default
- file.
- This feature is not used at the time of meshing.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-PRINT_SOURCE_TIME_FUNCTION
-\family default
- Turn this flag on to print information about the source time function in
- the file
-\family typewriter
-OUTPUT_FILES/plot_source_time_function.txt
-\family default
-.
- This feature is not used at the time of meshing.
-
-\end_layout
-
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-
-\end_inset
-
-
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-\align center
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-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Sample choices for
-\begin_inset Formula $\nexxi$
-\end_inset
-
- given
-\begin_inset Formula $\nprocxi$
-\end_inset
-
- based upon the relationship
-\begin_inset Formula $\nexxi=8\times c\times\nprocxi$
-\end_inset
-
-, where the integer
-\begin_inset Formula $c\ge1$
-\end_inset
-
-.
- The number of MPI slices, i.e., the total number of required processors,
- is
-\begin_inset Formula $6\times\nprocxi^{2}$
-\end_inset
-
-, as illustrated in Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "figure:mpi_slices"
-
-\end_inset
-
-.
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- for a given value of
-\begin_inset Formula $\nexxi$
-\end_inset
-
- can be estimated by running the small serial program
-\family typewriter
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-.
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-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Finally, you 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
-\family typewriter
-mymachines
-\family default
-.
- This file is not used by the mesher or solver, but is required by the
-\family typewriter
-go_mesher
-\family default
- and
-\family typewriter
-go_solver
-\family default
- default job submission scripts.
- See Chapter
-\begin_inset LatexCommand ref
-reference "cha:Running-Scheduler"
-
-\end_inset
-
- for information about running the code on a system with a scheduler, e.g.,
- LSF.
-\end_layout
-
-\begin_layout Standard
-Now that you have set the appropriate parameters in the
-\family typewriter
-Par_file
-\family default
- and have compiled the mesher, you are ready to launch it! This is most
- easily accomplished based upon the
-\family typewriter
-go_mesher
-\family default
- script.
- When you run on a PC cluster, the script assumes that the nodes are named
- n001, n002, etc.
- If this is not the case, change the
-\family typewriter
-tr -d `n'
-\family default
- line in the script.
- You may also need to edit the last command at the end of the script that
- invokes the
-\family typewriter
-mpirun
-\family default
- command.
-\end_layout
-
-\begin_layout Standard
-Mesher output is provided in the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory in
-\family typewriter
-output_mesher.txt
-\family default
-; this file provides lots of details about the mesh that was generated.
- Alternatively, output can be directed to the screen instead by uncommenting
- a line in
-\family typewriter
-constants.h
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-! uncomment this to write messages to the screen
-\end_layout
-
-\begin_layout LyX-Code
-! integer, parameter :: IMAIN = ISTANDARD_OUTPUT
-\end_layout
-
-\begin_layout Standard
-Note that on very fast machines, writing to the screen may slow down the
- code.
-\end_layout
-
-\begin_layout Standard
-Another file generated by the mesher is the header file
-\family typewriter
-OUTPUT_FILES/values_from_mesher.h
-\family default
-.
- 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.
-\end_layout
-
-\begin_layout Standard
-For a given model, set of nodes, and set of parameters in
-\family typewriter
-Par_file
-\family default
-, 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).
-\end_layout
-
-\begin_layout Standard
-Please note that it is difficult to correctly sample S waves in the inner
- core of the Earth because S-wave velocity is very small there.
- Therefore, correctly sampling S waves in the inner core would require a
- very dense mesh, which in turn would drastically reduce the time step of
- the explicit time scheme because the P wave velocity is very high in the
- inner core (Poisson's ratio is roughly equal to 0.44).
- Because shear wave attenuation is very high in the inner core (
-\begin_inset Formula $Q_{\mu}$
-\end_inset
-
- is approximately equal to 85), we have therefore decided to design the
- inner core mesh such that P waves are very well sampled but S waves are
- right at the sampling limit or even slightly below.
- This works fine because spurious numerical oscillations due to S-wave subsampli
-ng are almost completely suppressed by attenuation.
- However, this implies that one should not use SPECFEM3D_GLOBE with the
- regular mesh and period estimates of Table
-\begin_inset LatexCommand ref
-reference "table:nex"
-
-\end_inset
-
- to study the PKJKP phase very precisely.
- If one is interested in that phase, one should use typically 1.5 times to
- twice the number of elements NEX indicated in the table.
-\end_layout
-
-\begin_layout Standard
-Regarding fluid/solid coupling at the CMB and ICB, in SPECFEM3D_GLOBE we
- do not use the fluid-solid formulation of
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02a}
-\end_layout
-
-\end_inset
-
- and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02b}
-\end_layout
-
-\end_inset
-
- anymore, we now use a displacement potential in the fluid (rather than
- a velocity potential as in
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02a}
-\end_layout
-
-\end_inset
-
- and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02b}
-\end_layout
-
-\end_inset
-
-).
- This leads to the simpler fluid-solid matching condition introduced by
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{ChVa04}
-\end_layout
-
-\end_inset
-
- with no numerical iterations at the CMB and ICB.
-\end_layout
-
-\begin_layout Standard
-For accuracy reasons, in the mesher the coordinates of the mesh points (arrays
- xstore, ystore and zstore) are always created in double precision.
- If the solver is compiled in single precision mode, the mesh coordinates
- are converted to single precision before being saved in the local mesh
- files.
-\end_layout
-
-\begin_layout Section
-Memory requirements
-\end_layout
-
-\begin_layout Standard
-The SPECFEM3D_GLOBE memory requirements can be estimated before or after
- running the mesher using the small serial program
-\family typewriter
-\size small
-xcreate_header_file
-\family default
-\size default
-, which reads the input file
-\family typewriter
-\size small
-DATA/Par_file
-\family default
-\size default
- and displays the total amount of memory that will be needed by the mesher
- and the solver to run it.
- This way, users can easily modify the parameters and check that their simulatio
-n will fit in memory on their machine.
- The file created by
-\family typewriter
-\size small
-xcreate_header_file
-\family default
-\size default
- is called
-\family typewriter
-OUTPUT_FILES/values_from_mesher.h
-\family default
- and contains even more details about the future simulation.
-\end_layout
-
-\begin_layout Section
-Checking the MPI Buffers (Optional)
-\end_layout
-
-\begin_layout Standard
-The mesher writes MPI communication tables in the
-\family typewriter
-OUTPUT_FILES
-\family default
- subdirectory in the files
-\family typewriter
-addressing.txt
-\family default
-,
-\family typewriter
-list_messages_corners.txt
-\family default
- and
-\family typewriter
-list_messages_faces.txt
-\family default
-, and MPI communication buffers to the local disks.
- Use the four serial codes
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-check_buffers_2D.f90
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-check_buffers_1D.f90
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-check_buffers_faces_chunks.f90
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-check_buffers_corners_chunks.f90
-\family default
-
-\end_layout
-
-\begin_layout Standard
-to check that all the MPI buffers created by the mesher have been generated
- correctly.
- For example, typing `
-\family typewriter
-make check_buffers_2D
-\family default
-' and then `
-\family typewriter
-xcheck_buffers_2D
-\family default
-' checks the communication buffers between faces common to the mesh slices.
- `
-\family typewriter
-xcheck_buffers_1D
-\family default
-' checks the communication buffers between edges common to the mesh slices.
- `
-\family typewriter
-xcheck_buffers_faces_chunks
-\family default
-' checks the communication buffers between faces common to the mesh chunks,
- i.e., the faces of the six blocks of the cubed-sphere mesh.
- `
-\family typewriter
-xcheck_buffers_corners_chunks
-\family default
-' checks the communication buffers between edges common to the mesh chunks,
- which must be treated separately in MPI because they are of valence 3 (i.e.,
- they are shared between three chunks).
-
-\end_layout
-
-\begin_layout Standard
-Please note that running these codes is optional because no information
- needed by the solver is generated.
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Checking-the-Mesh"
-
-\end_inset
-
-Checking the Mesh Quality (Optional)
-\end_layout
-
-\begin_layout Standard
-The quality of the mesh may be analyzed based on the serial code
-\family typewriter
-check_mesh_quality_AVS_DX.f90
-\family default
-.
- Type `
-\family typewriter
-make check_mesh_quality_AVS_DX
-\family default
-' and then use `
-\family typewriter
-xcheck_mesh_quality_AVS_DX
-\family default
-' to generate an AVS output file (
-\family typewriter
-AVS_meshquality.inp
-\family default
- in AVS UCD format) or an OpenDX output file (
-\family typewriter
-DX_meshquality.dx
-\family default
-) that can be used to investigate mesh quality, for example, skewness of
- elements and a Gnuplot histogram (
-\family typewriter
-mesh_quality
-\newline
-_histogram.txt
-\family default
-) that can be plotted with gnuplot (type `
-\family typewriter
-gnuplot plot_mesh_quality_histogram.gnu
-\family default
-').
- 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.
-
-\end_layout
-
-\begin_layout Standard
-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.
-
-\end_layout
-
-\begin_layout Standard
-Also note that running this code is optional because no information needed
- by the solver is generated.
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Running-the-Solver"
-
-\end_inset
-
-Running the Solver
-\family typewriter
-xspecfem3D
-\end_layout
-
-\begin_layout Standard
-Now that you have successfully run the mesher, you are ready to compile
- the solver.
- For reasons of speed, the solver uses static memory allocation.
- Therefore it needs to be recompiled (type `
-\family typewriter
-make clean
-\family default
-' and `
-\family typewriter
-make specfem3D
-\family default
-') every time one reruns the mesher with different parameters.
- To compile the solver one needs a file generated by the mesher in the directory
-
-\family typewriter
-OUTPUT_FILES
-\family default
- called
-\family typewriter
-values_from_mesher.h
-\family default
-, which contains parameters describing the static size of the arrays as
- well as the setting of certain flags.
-\end_layout
-
-\begin_layout Standard
-The solver needs three input files in the
-\family typewriter
-DATA
-\family default
- directory to run: the
-\family typewriter
-Par_file
-\family default
- that was discussed in detail in Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Running-the-Mesher"
-
-\end_inset
-
-, the earthquake source parameter file
-\family typewriter
-CMTSOLUTION
-\family default
-, and the stations file
-\family typewriter
-STATIONS
-\family default
-.
- Most parameters in the
-\family typewriter
-Par_file
-\family default
- should be set prior to running the mesher.
- Only the following parameters may be changed after running the mesher:
-\end_layout
-
-\begin_layout Itemize
-the simulation type control parameters:
-\family typewriter
-SIMULATION_TYPE
-\family default
- and
-\family typewriter
-SAVE_FORWARD
-\end_layout
-
-\begin_layout Itemize
-the record length
-\family typewriter
-RECORD_LENGTH_IN_MINUTES
-\end_layout
-
-\begin_layout Itemize
-the movie control parameters
-\family typewriter
-MOVIE_SURFACE
-\family default
-,
-\family typewriter
-MOVIE_VOLUME
-\family default
-, and
-\family typewriter
-NTSTEPS_BETWEEN_FRAMES
-\end_layout
-
-\begin_layout Itemize
-the multi-stage simulation parameters
-\family typewriter
-NUMBER_OF_RUNS
-\family default
- and
-\family typewriter
-NUMBER_OF_THIS_RUN
-\end_layout
-
-\begin_layout Itemize
-the output information parameters
-\family typewriter
-NTSTEP_BETWEEN_OUTPUT_INFO, NTSTEP_BETWEEN_OUTPUT_
-\newline
-SEISMOS, OUTPUT_SEISMOS_ASCII_
-TEXT, OUTPUT_SEISMOS_SAC_ALPHANUM, OUTPUT_
-\newline
-SEISMOS_SAC_BINARY and ROTATE_SEISMOGR
-AMS_RT
-\end_layout
-
-\begin_layout Itemize
-the
-\family typewriter
-RECEIVERS_CAN_BE_BURIED
-\family default
- and
-\family typewriter
-PRINT_SOURCE_TIME_FUNCTION
-\family default
- flags
-\end_layout
-
-\begin_layout Standard
-Any other change to the
-\family typewriter
-Par_file
-\family default
- implies rerunning both the mesher and the solver.
-\end_layout
-
-\begin_layout Standard
-For any particular earthquake, the
-\family typewriter
-CMTSOLUTION
-\family default
- file that represents the point source may be obtained directly from the
-
-\begin_inset LatexCommand htmlurl
-name "Harvard Centroid-Moment Tensor (CMT) web page"
-target "www.seismology.harvard.edu"
-
-\end_inset
-
-.
- It looks like this:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-
-\size small
-\begin_inset Graphics
- filename figures/Denali_CMT.eps
- width 100text%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-
-\family typewriter
-CMTSOLUTION
-\family default
- file obtained from the Harvard CMT catalog.
- The top line is the initial estimate of the source, which is used as a
- starting point for the CMT solution.
-
-\series bold
-M
-\series default
- is the moment tensor,
-\begin_inset Formula $M_{0}$
-\end_inset
-
-
-\size small
-
-\size default
-is the seismic moment, and
-\begin_inset Formula $M_{w}$
-\end_inset
-
- is the moment magnitude.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:CMTSOLUTION-file"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The
-\family typewriter
-CMTSOLUTION
-\family default
- should be edited in the following way:
-\end_layout
-
-\begin_layout Itemize
-Set the
-\family typewriter
-time shift
-\family default
- parameter equal to
-\begin_inset Formula $0.0$
-\end_inset
-
- (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
-\begin_inset LatexCommand ref
-reference "sec:Process-data-and-syn"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Itemize
-For point-source simulations (see finite sources, page
-\begin_inset LatexCommand pageref
-reference "To-simulate-a"
-
-\end_inset
-
-) we recommend setting the source half-duration parameter
-\family typewriter
-half duration
-\family default
- equal to zero, which corresponds to simulating a step source-time function,
- i.e., a moment-rate function that is a delta function.
- If
-\family typewriter
-half duration
-\family default
- is not set to zero, the code will use a Gaussian (i.e., a signal with a shape
- similar to a `smoothed triangle', as explained in
-\begin_inset LatexCommand cite
-key "KoTr02a"
-
-\end_inset
-
- and shown in Fig\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:gauss.vs.triangle"
-
-\end_inset
-
-) source-time function with half-width
-\family typewriter
-half duration
-\family default
-.
- We prefer to run the solver with
-\family typewriter
-half duration
-\family default
- set to zero and convolve the resulting synthetic seismograms in post-processing
- after the run, because this way it is easy to use a variety of source-time
- functions (see Section
-\begin_inset LatexCommand ref
-reference "sec:Process-data-and-syn"
-
-\end_inset
-
-).
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{KoTr02a}
-\end_layout
-
-\end_inset
-
- determined that the noise generated in the simulation by using a step source
- time function may be safely filtered out afterward based upon a convolution
- with the desired source time function and/or low-pass filtering.
- Use the postprocessing script
-\family typewriter
-process_syn.pl
-\family default
- (see Section
-\begin_inset LatexCommand ref
-reference "sub:process_syn.pl"
-
-\end_inset
-
-) with the
-\family typewriter
--h
-\family default
- flag, or the serial code
-\family typewriter
-convolve_source_timefunction.f90
-\family default
- and the script
-\family typewriter
-UTILS/convolve_source_timefunction.csh
-\family default
- for this purpose, or alternatively use signal-processing software packages
- such as
-\begin_inset LatexCommand htmlurl
-name "SAC"
-target "www.llnl.gov/sac"
-
-\end_inset
-
-.
- Type
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-
-\family typewriter
-make convolve_source_timefunction
-\end_layout
-
-\begin_layout Standard
-to compile the code and then set the parameter
-\family typewriter
-hdur
-\family default
- in
-\family typewriter
-UTILS/convolve_source_timefunction.csh
-\family default
- to the desired half-duration.
-
-\end_layout
-
-\end_deeper
-\begin_layout Itemize
-The zero time of the simulation corresponds to the center of the triangle/Gaussi
-an, or the centroid time of the earthquake.
- The start time of the simulation is
-\begin_inset Formula $t=-1.5*\texttt{half duration}$
-\end_inset
-
- (the 1.5 is to make sure the moment rate function is very close to zero
- when starting the simulation).
- To convert to absolute time
-\begin_inset Formula $t_{\mathrm{abs}}$
-\end_inset
-
-, set
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-\begin_inset Formula $t_{\mathrm{abs}}=t_{\mathrm{pde}}+\texttt{time shift}+t_{\mathrm{synthetic}}$
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-where
-\begin_inset Formula $t_{\mathrm{pde}}$
-\end_inset
-
- is the time given in the first line of the
-\family typewriter
-CMTSOLUTION
-\family default
-,
-\family typewriter
-time shift
-\family default
- is the corresponding value from the original
-\family typewriter
-CMTSOLUTION
-\family default
- file and
-\begin_inset Formula $t_{\mathrm{synthetic}}$
-\end_inset
-
- is the time in the first column of the output seismogram.
-\end_layout
-
-\end_deeper
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/gauss_vs_triangle_mod.eps
- width 3in
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Comparison of the shape of a triangle and the Gaussian function actually
- used.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:gauss.vs.triangle"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Centroid latitude and longitude should be provided in geographical coordinates.
- The code converts these coordinates to geocentric coordinates\InsetSpace ~
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{DaTr98}
-\end_layout
-
-\end_inset
-
-.
- Of course you may provide your own source representations by designing
- your own
-\family typewriter
-CMTSOLUTION
-\family default
- file.
- Just make sure that the resulting file adheres to the Harvard CMT conventions
- (see Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Reference-Frame-Convention"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "To-simulate-a"
-
-\end_inset
-
-To simulate a kinematic rupture, i.e., a finite-source event, represented
- in terms of
-\begin_inset Formula $N_{\mathrm{sources}}$
-\end_inset
-
- point sources, provide a
-\family typewriter
-CMTSOLUTION
-\family default
- file that has
-\begin_inset Formula $N_{\mathrm{sources}}$
-\end_inset
-
- entries, one for each subevent (i.e., concatenate
-\begin_inset Formula $N_{\mathrm{sources}}$
-\end_inset
-
-
-\family typewriter
-CMTSOLUTION
-\family default
- files to a single
-\family typewriter
-CMTSOLUTION
-\family default
- file).
- At least one entry (not necessarily the first) must have a zero
-\family typewriter
-time shift
-\family default
-, and all the other entries must have non-negative
-\family typewriter
-time shift
-\family default
-.
- Each subevent can have its own half duration, latitude, longitude, depth,
- and moment tensor (effectively, the local moment-density tensor).
-\end_layout
-
-\begin_layout Standard
-Note that the zero in the synthetics does NOT represent the hypocentral
- time or centroid time in general, but the timing of the
-\shape italic
-center
-\shape default
- of the source triangle with zero
-\family typewriter
-time shift
-\family default
- (Fig\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:source_timing"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-Although it is convenient to think of each source as a triangle, in the
- simulation they are actually Gaussians (as they have better frequency character
-istics).
- The relationship between the triangle and the Gaussian used is shown in
- Fig\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:gauss.vs.triangle"
-
-\end_inset
-
-.
- For finite fault simulations it is usually not advisable to use a zero
- half duration and convolve afterwards, since the half duration is generally
- fixed by the finite fault model.
-\end_layout
-
-\begin_layout Standard
-
-\size small
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\noindent
-\align center
-
-\size small
-\begin_inset Graphics
- filename figures/source_timing.eps
- width 5in
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Example of timing for three sources.
- The center of the first source triangle is defined to be time zero.
- Note that this is NOT in general the hypocentral time, or the start time
- of the source (marked as tstart).
- The parameter
-\family typewriter
-time shift
-\family default
- in the
-\family typewriter
-CMTSOLUTION
-\family default
- file would be t1(=0), t2, t3 in this case, and the parameter
-\family typewriter
-half duration
-\family default
- would be hdur1, hdur2, hdur3 for the sources 1, 2, 3 respectively.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\size small
-\begin_inset LatexCommand label
-name "fig:source_timing"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The solver can calculate seismograms at any number of stations for basically
- the same numerical cost, so the user is encouraged to include as many stations
- as conceivably useful in the
-\family typewriter
-STATIONS
-\family default
- file, which looks like this:
-\end_layout
-
-\begin_layout Standard
-
-\size small
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\noindent
-\align center
-
-\size small
-\begin_inset Graphics
- filename figures/STATIONS_global_explained.eps
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Sample
-\family typewriter
-STATIONS
-\family default
- file.
- Station latitude and longitude should be provided in geographical coordinates.
- The width of the station label should be no more than 32 characters (see
-
-\family typewriter
-MAX_LENGTH_STATION_NAME
-\family default
- in the
-\family typewriter
-constants.h
-\family default
- file), and the network label should be no more than 8 characters (see
-\family typewriter
-MAX_LENGTH_NETWORK_NAME
-\family default
- in the
-\family typewriter
-constants.h
-\family default
- file).
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Each line represents one station in the following format:
-\end_layout
-
-\begin_layout LyX-Code
-\noindent
-
-\size small
-Station Network Latitude (degrees) Longitude (degrees) Elevation (m) burial
- (m)
-\end_layout
-
-\begin_layout Standard
-Solver output is provided in the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory in the
-\family typewriter
-output_solver.txt
-\family default
- file.
- Output can be directed to the screen instead by uncommenting a line in
-
-\family typewriter
-constants.h
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-! uncomment this to write messages to the screen
-\end_layout
-
-\begin_layout LyX-Code
-! integer, parameter :: IMAIN = ISTANDARD_OUTPUT
-\end_layout
-
-\begin_layout Standard
-Note that on very fast machines, writing to the screen may slow down the
- code.
-\end_layout
-
-\begin_layout Standard
-While the solver is running, its progress may be tracked by monitoring the
- `
-\family typewriter
-timestamp*
-\family default
-' files in the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory.
- These tiny files look something like this:
-\end_layout
-
-\begin_layout LyX-Code
-Time step # 200
-\end_layout
-
-\begin_layout LyX-Code
-Time: 0.6956667 minutes
-\end_layout
-
-\begin_layout LyX-Code
-Elapsed time in seconds = 252.6748970000000
-\end_layout
-
-\begin_layout LyX-Code
-Elapsed time in hh:mm:ss = 0 h 04 m 12 s
-\end_layout
-
-\begin_layout LyX-Code
-Mean elapsed time per time step in seconds = 1.263374485000000
-\end_layout
-
-\begin_layout LyX-Code
-Max norm displacement vector U in solid in all slices (m) = 1.9325
-\end_layout
-
-\begin_layout LyX-Code
-Max non-dimensional potential Ufluid in fluid in all slices = 1.1058885E-22
-
-\end_layout
-
-\begin_layout Standard
-The
-\family typewriter
-timestamp*
-\family default
- files provide the
-\family typewriter
-Mean elapsed time per time step in seconds
-\family default
-, which may be used to assess performance on various machines (assuming
- you are the only user on a node), as well as the
-\family typewriter
-\size small
-Max
-\family default
-
-\family typewriter
-norm
-\family default
-
-\family typewriter
-displacement
-\family default
-
-\family typewriter
-vector
-\family default
-
-\family typewriter
-U
-\family default
-
-\family typewriter
-in
-\family default
-
-\family typewriter
-solid
-\family default
-
-\family typewriter
-in
-\family default
-
-\family typewriter
-all
-\family default
-
-\family typewriter
-slices\InsetSpace ~
-(m)
-\family default
-
-\family typewriter
-and
-\family default
-
-\family typewriter
-Max
-\family default
-
-\family typewriter
-non-dimensional
-\family default
-
-\family typewriter
-potential
-\family default
-
-\family typewriter
-Ufluid
-\family default
-
-\family typewriter
-in
-\family default
-
-\family typewriter
-fluid
-\family default
-
-\family typewriter
-in
-\family default
-
-\family typewriter
-all
-\family default
-
-\family typewriter
-slices
-\family default
-\size default
-.
- If something is wrong with the model, the mesh, or the source, you will
- see the code become unstable through exponentionally growing values of
- the displacement and/or fluid potential with time, and ultimately the run
- will be terminated by the program when either of these values becomes greater
- than
-\family typewriter
-STABILITY_THRESHOLD
-\family default
- defined in
-\family typewriter
-constants.h
-\family default
-.
- You can control the rate at which the timestamp files are written based
- upon the parameter
-\family typewriter
-NTSTEP_BETWEEN_OUTPUT_INFO
-\family default
- in the
-\family typewriter
-Par_file
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-Having set the
-\family typewriter
-Par_file
-\family default
- parameters, and having provided the
-\family typewriter
-CMTSOLUTION
-\family default
- and
-\family typewriter
-STATIONS
-\family default
- files, you are now ready to launch the solver! This is most easily accomplished
- based upon the
-\family typewriter
-go_solver
-\family default
- script (see Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Running-Scheduler"
-
-\end_inset
-
- for information about running the code through a scheduler, e.g., LSF).
- You may need to edit the last command at the end of the script that invokes
- the
-\family typewriter
-mpirun
-\family default
- command.
- Another option is to use the
-\family typewriter
-runall
-\family default
- script, which compiles and runs both mesher and solver in sequence.
- This is a safe approach that ensures using the correct combination of mesher
- output and solver input.
-\end_layout
-
-\begin_layout Standard
-It is important to realize that the CPU and memory requirements of the solver
- are closely tied to choices about attenuation (
-\family typewriter
-ATTENUATION
-\family default
-) and the nature of the model (i.e., isotropic models are cheaper than anisotropic
- models).
- We encourage you to run a variety of simulations with various flags turned
- on or off to develop a sense for what is involved.
-\end_layout
-
-\begin_layout Standard
-For the same model, one can rerun the solver for different events by simply
- changing the
-\family typewriter
-CMTSOLUTION
-\family default
- file, and/or for different stations by changing the
-\family typewriter
-STATIONS
-\family default
- file.
- There is no need to rerun the mesher.
- Of course it is best to include as many stations as possible, since this
- does not add significantly to the cost of the simulation.
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Regional-Simulations"
-
-\end_inset
-
-Regional Simulations
-\end_layout
-
-\begin_layout Standard
-The code has the option of running in 1-, 2-, 3- or 6-chunk mode.
- The 1- or 2-chunk options may be used for higher resolution regional simulation
-s.
- A one-chunk mesh may have lateral dimensions other than the customary
-\begin_inset Formula $90^{\circ}$
-\end_inset
-
- per chunk, which can further increase the resolution of the mesh, and thus
- reduce the shortest period in the synthetic seismograms (but of course
- then also reducing the time step in order for the simulation to remain
- stable).
- A disadvantage of regional simulations is that one needs to use approximate
- absorbing boundary conditions on the side and bottom edges of the model
- (e.g., see
-\begin_inset LatexCommand cite
-key "KoTr99"
-
-\end_inset
-
- for a description of the paraxial boundary conditions used).
- Figure\InsetSpace ~
-
-\begin_inset LatexCommand vref
-reference "fig:3D-spectral-element-mesh"
-
-\end_inset
-
- and Figure\InsetSpace ~
-
-\begin_inset LatexCommand vref
-reference "fig:Close-up-view-of"
-
-\end_inset
-
- show an example of a one-chunk mesh centered on the Japan subduction zone,
- applied in the Japan regional waveform simulation
-\begin_inset LatexCommand citep
-key "ChTrHeKa07"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Section
-One-Chunk Simulations
-\begin_inset LatexCommand label
-name "sec:One-Chunk-Simulations"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-For a one-chunk regional simulation the following parameters need to be
- set in the
-\family typewriter
-Par_file
-\family default
-:
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nchunks$
-\end_inset
-
- Must be set to 1.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ANGULAR_WIDTH_XI_IN_DEGREES
-\family default
- Denotes the width of one side of the chunk (
-\begin_inset Formula $90^{\circ}$
-\end_inset
-
-or less).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ANGULAR_WIDTH_ETA_IN_DEGREES
-\family default
- Denotes the width of the second side of the chunk (
-\begin_inset Formula $90^{\circ}$
-\end_inset
-
-or less).
- Note that this value may be different from
-\family typewriter
-ANGULAR_WIDTH_XI_IN_DEGREES
-\family default
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-CENTER_LATITUDE_IN_DEGREES
-\family default
- Defines the latitude of the center of the chunk (degrees).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-CENTER_LONGITUDE_IN_DEGREES
-\family default
- Defines the longitude of the center of the chunk (degrees).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-GAMMA_ROTATION_AZIMUTH
-\family default
- Defines the rotation angle of the chunk about its center measured counter
- clockwise from due North (degrees).
- The corners of the mesh are output in
-\family typewriter
-\size small
-OUTPUT_FILES/values_from_mesher.h
-\family default
-\size default
-.
- The output corner progression in
-\family typewriter
-\size small
-OUTPUT_FILES/values_from_mesher.h
-\family default
-\size default
- is bottom left, bottom right, top left, top right.
- The rotation azimuth can be changed in the
-\family typewriter
-Par_file
-\family default
- and the corners output
-\family typewriter
-(
-\size small
-OUTPUT_FILES/
-\newline
-values_from_mesher.h
-\size default
-)
-\family default
- by using
-\size small
-
-\family typewriter
-xcreate_header_file
-\family default
-\size default
-.
- It is important to note that the mesher or the solver does not need to
- be run to determine the limits of a 1-chunk simulation.
-
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nexxi$
-\end_inset
-
- The number of spectral elements along the
-\begin_inset Formula $\xi$
-\end_inset
-
- side of the chunk.
- This number
-\shape italic
-must
-\shape default
- be 8\InsetSpace ~
-
-\begin_inset Formula $\times$
-\end_inset
-
-\InsetSpace ~
-a multiple of
-\begin_inset Formula $\nprocxi$
-\end_inset
-
- defined below.
- For a
-\begin_inset Formula $90^{\circ}$
-\end_inset
-
- chunk, we do not recommend using
-\begin_inset Formula $\nexxi$
-\end_inset
-
- less than\InsetSpace ~
-64 because the curvature of the Earth cannot be honored if one
- uses too few elements, which results in inaccurate and unstable simulations.
-
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nexeta$
-\end_inset
-
- The number of spectral elements along the
-\begin_inset Formula $\eta$
-\end_inset
-
- side of the chunk.
- This number
-\shape italic
-must
-\shape default
- be 8\InsetSpace ~
-
-\begin_inset Formula $\times$
-\end_inset
-
-\InsetSpace ~
-a multiple of
-\begin_inset Formula $\nproceta$
-\end_inset
-
- defined below.
- Note that in order to get elements that are close to square on the Earth's
- surface, the following ratios should be similar:
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-\begin_inset Formula $\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}/\nexxi$
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-\begin_inset Formula $\texttt{ANGULAR\_WIDTH\_ETA\_IN\_DEGREES}/\nexeta$
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-Because of the geometry of the cubed sphere, the option of having different
- values for
-\begin_inset Formula $\nexxi$
-\end_inset
-
- and
-\begin_inset Formula $\nexeta$
-\end_inset
-
- is available only for regional simulations when
-\begin_inset Formula $\nchunks=1$
-\end_inset
-
- (1/6th of the sphere).
-
-\family default
-
-\end_layout
-
-\end_deeper
-\begin_layout Description
-\begin_inset Formula $\nprocxi$
-\end_inset
-
- The number of processors or mesh slices along the
-\begin_inset Formula $\xi$
-\end_inset
-
- side of the chunk.
- To accommodate the mesh doubling layers, we must have
-\begin_inset Formula $\nexxi=8\times c\times\nprocxi$
-\end_inset
-
-, where
-\begin_inset Formula $c\ge1$
-\end_inset
-
- is a positive integer.
- See Table\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "table:nex"
-
-\end_inset
-
- for various suitable choices.
-
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nproceta$
-\end_inset
-
- The number of processors or slices along the
-\begin_inset Formula $\eta$
-\end_inset
-
- side of the chunk; we must have
-\begin_inset Formula $\nexeta=8\times c\times\nproceta$
-\end_inset
-
-, where
-\begin_inset Formula $c\ge1$
-\end_inset
-
- is a positive integer.
-
-\begin_inset Formula $\nprocxi$
-\end_inset
-
- and
-\begin_inset Formula $\nproceta$
-\end_inset
-
- must be equal when
-\begin_inset Formula $\nchunks=6$
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\align center
-\begin_inset Graphics
- filename figures/fig5a.jpg
- lyxscale 35
- scale 65
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-
-\series bold
-\begin_inset LatexCommand label
-name "fig:3D-spectral-element-mesh"
-
-\end_inset
-
-
-\series default
-S-wave velocity anomalies from the global tomographic model s20rts
-\begin_inset LatexCommand citep
-key "RiVa00"
-
-\end_inset
-
- are superimposed on the mesh.
- For parallel computing purposes, the one-chunk SEM simulation is subdivided
- in terms of 64 slices.
- The center of the chunk is at (38.5
-\begin_inset Formula $^{\circ}$
-\end_inset
-
- N, 137.5
-\begin_inset Formula $^{\circ}$
-\end_inset
-
- E), and the lateral dimensions are 30
-\begin_inset Formula $^{\circ}$
-\end_inset
-
-
-\begin_inset Formula $\times$
-\end_inset
-
- 30
-\begin_inset Formula $^{\circ}$
-\end_inset
-
-.
- Two doubling layers are indicated at a depth of 25\InsetSpace ~
-km (PREM Moho depth)
- and a depth of about 1650\InsetSpace ~
-km.
- Shows full view of 25 neighboring slices; see Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Close-up-view-of"
-
-\end_inset
-
- for close-up of upper mantle mesh.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\align center
-\begin_inset Graphics
- filename figures/fig5b.jpg
- lyxscale 35
- scale 65
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-
-\series bold
-\begin_inset LatexCommand label
-name "fig:Close-up-view-of"
-
-\end_inset
-
-
-\series default
-Close-up view of the upper mantle mesh shown in Figure\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:3D-spectral-element-mesh"
-
-\end_inset
-
-.
- Note that the element size in the crust (top layer) is 13\InsetSpace ~
-km
-\begin_inset Formula $\times$
-\end_inset
-
- 13\InsetSpace ~
-km, and that the size of the spectral elements is doubled in the upper
- mantle.
- The velocity variation is captured by NGLL = 5 grid points in each direction
- of the elements
-\begin_inset LatexCommand citep
-key "KoTr02a,KoTr02b"
-
-\end_inset
-
-.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ABSORBING_CONDITIONS
-\family default
- Set to
-\family typewriter
-.true.
-
-\family default
-\size small
-
-\size default
-for regional simulations.
- For instance, see
-\begin_inset LatexCommand citet
-key "KoTr99"
-
-\end_inset
-
- for a description of the paraxial boundary conditions used.
- Note that these conditions are never perfect, and in particular surface
- waves may partially reflect off the artificial boundaries.
- Note also that certain arrivals, e.g., PKIKPPKIKP, will be missing from the
- synthetics.
-
-\end_layout
-
-\begin_layout Standard
-When the width of the chunk is different from
-\begin_inset Formula $90^{\circ}$
-\end_inset
-
- (or the number of elements is greater than 1248), the radial distribution
- 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
-\family typewriter
-check_mesh_quality_AVS_DX.f90
-\family default
- to check the quality of the mesh (see Section\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Checking-the-Mesh"
-
-\end_inset
-
-).
- 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:
-\end_layout
-
-\begin_layout Standard
-\begin_inset Formula \[
-\omega_{max}=\omega_{min}\times10^{W_{3}}\]
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-where
-\begin_inset Formula $W_{3}$
-\end_inset
-
- is the optimal width in frequency for 3 Standard Linear Solids, about 1.75.
- See
-\family typewriter
-\size small
-read_compute_parameters.f90
-\family default
-\size default
- for more details.
-\end_layout
-
-\begin_layout Standard
-The time stepping is determined in a similar fashion as Equation (48) in
-
-\begin_inset LatexCommand citet
-key "KoTr02a"
-
-\end_inset
-
-:
-\end_layout
-
-\begin_layout LyX-Code
-dt =
-\begin_inset Formula $S_{c}$
-\end_inset
-
- Element Width in km (
-\begin_inset Formula $r=$
-\end_inset
-
-ICB) / Velocity (
-\begin_inset Formula $r=$
-\end_inset
-
-ICB)
-\end_layout
-
-\begin_layout Standard
-where
-\begin_inset Formula $S_{c}$
-\end_inset
-
- is the stability condition (about 0.4).
- We use the radius at the inner core boundary because this is where the
- maximum velocity/element width occurs.
- Again, see
-\family typewriter
-\size small
-read_compute_parameters
-\size default
-.f90
-\family default
- for all the details.
-
-\end_layout
-
-\begin_layout Standard
-The approximate shortest period at which a regional simulation is accurate
- may be determined based upon the relation
-\begin_inset Formula \begin{equation}
-\mbox{shortest period (s)}\simeq(256/\nexxi)\times(\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}/90)\times17.\label{eq:shortest_period_regional}\end{equation}
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-Two-Chunk Simulations
-\end_layout
-
-\begin_layout Standard
-For a two-chunk regional simulation the following parameters need to be
- set in the
-\family typewriter
-Par_file
-\family default
-:
-\end_layout
-
-\begin_layout Description
-\begin_inset Formula $\nchunks$
-\end_inset
-
- Must be set to 2
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ANGULAR_WIDTH_XI_IN_DEGREES
-\family default
- Denotes the width of one side of the chunk, and it has to be 90 degrees.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-ANGULAR_WIDTH_ETA_IN_DEGREES
-\family default
- Denotes the width of the second side of the chunk, and it also has to be
- 90 degrees.
-
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-NEX_XI
-\family default
- and
-\family typewriter
-NEX_ETA
-\family default
- follow the same description in Section
-\begin_inset LatexCommand ref
-reference "sec:One-Chunk-Simulations"
-
-\end_inset
-
-, however, they need to be the same in this case.
- All other parameters are similar to the one-chunk simulations, refer to
- Section
-\begin_inset LatexCommand ref
-reference "sec:One-Chunk-Simulations"
-
-\end_inset
-
- for details.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/2-chunk-surface.eps
- lyxscale 60
- width 60text%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Geometry of a 2-chunk simulation, where the first chunk (
-\family typewriter
-CHUNK_AB
-\family default
-) centers at
-\begin_inset Formula $40^{\circ}$
-\end_inset
-
- latitude,
-\begin_inset Formula $10^{\circ}$
-\end_inset
-
- longitude, and has been rotated by
-\begin_inset Formula $20^{\circ}$
-\end_inset
-
- counter clockwise, and the second chunk (
-\family typewriter
-CHUNK_AC
-\family default
-) connects to the first chunk through one face.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Adjoint-Simulations"
-
-\end_inset
-
-Adjoint Simulations
-\end_layout
-
-\begin_layout Standard
-Adjoint simulations are generally performed for two distinct applications.
- First, they can be used for earthquake source inversions, especially earthquake
-s with large ruptures such as the Sumatra-Andaman event
-\begin_inset LatexCommand citep
-key "LayKanamoriAmmon2005,AmmonJiThio2005,ParkSongTromp2005"
-
-\end_inset
-
-.
- Second, they can be used to generate finite-frequency sensitivity kernels
- that are a critical part of tomographic inversions based upon 3D reference
- models
-\begin_inset LatexCommand citep
-key "trompetal2005,LiTr06,LiTr08"
-
-\end_inset
-
-.
- In either case, source parameter or velocity structure updates are sought
- to minimize a specific misfit function (e.g., waveform or traveltime differences)
-, and the adjoint simulation provides a means of computing the gradient
- of the misfit function and further reducing it in successive iterations.
- Applications and procedures pertaining to source studies and finite-frequency
- kernels are discussed in Sections\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Adjoint-simulation-sources"
-
-\end_inset
-
- and
-\begin_inset LatexCommand ref
-reference "sec:Adjoint-simulation-finite"
-
-\end_inset
-
-, respectively.
- The two related parameters in the
-\family typewriter
-Par_file
-\family default
- are
-\family typewriter
-SIMULATION_TYPE
-\family default
- (1, 2 or 3) and
-\family typewriter
-SAVE_FORWARD
-\family default
- (boolean).
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Adjoint-simulation-sources"
-
-\end_inset
-
-Adjoint Simulations for Sources
-\end_layout
-
-\begin_layout Standard
-In the case where a specific misfit function is minimized to invert for
- the earthquake source parameters, the gradient of the misfit function with
- respect to these source parameters can be computed by placing time-reversed
- seismograms at the receivers and using them as sources in an adjoint simulation
-, and then the value of the gradient is obtained from the adjoint seismograms
- recorded at the original earthquake location.
-
-\end_layout
-
-\begin_layout Enumerate
-
-\series bold
-Prepare the adjoint sources
-\series default
-
-\begin_inset LatexCommand label
-name "enu:Prepare-the-adjoint"
-
-\end_inset
-
-
-\end_layout
-
-\begin_deeper
-\begin_layout Enumerate
-First, run a regular forward simlation (
-\family typewriter
-SIMULATION_TYPE = 1
-\family default
- and
-\family typewriter
-SAVE_FORWARD = .false.
-\family default
-).
- You can automatically set these two variables using the
-\family typewriter
-\size small
-UTILS/change_simulation_type.pl
-\family default
-\size default
- script:
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-UTILS/change_simulation_type.pl -f
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-and then collect the recorded seismograms at all the stations given in
-\family default
-
-\family typewriter
-DATA/STATIONS
-\family roman
-.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-Then select the stations for which you want to compute the time-reversed
- adjoint sources and run the adjoint simulation, and compile them into the
-
-\family typewriter
-DATA/STATIONS_ADJOINT
-\family default
- file, which has the same format as the regular
-\family typewriter
-DATA/STATIONS
-\family default
- file.
-
-\end_layout
-
-\begin_deeper
-\begin_layout Itemize
-Depending on what type of misfit function is used for the source inversion,
- adjoint sources need to be computed from the original recorded seismograms
- for the selected stations and saved in the
-\family typewriter
-SEM/
-\family default
- directory with the format
-\family typewriter
-STA.NT.LH?.adj
-\family default
-, where
-\family typewriter
-STA
-\family default
-,
-\family typewriter
-NT
-\family default
- are the station name and network code given in the
-\family typewriter
-DATA/STATIONS_ADJOINT
-\family default
- file, and
-\family typewriter
-LH?
-\family default
- represents the component name of a particular adjoint seismogram.
-
-\end_layout
-
-\begin_layout Itemize
-The adjoint seismograms are in the same format as the original seismogram
- (
-\family typewriter
-STA.NT.LH?.sem?
-\family default
-), with the same start time, time interval and record length.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-Notice that even if you choose to time reverse only one component from one
- specific station, you still need to supply all three components because
- the code is expecting them (you can set the other two components to be
- zero).
-\end_layout
-
-\begin_layout Enumerate
-Also note that since time-reversal is done in the code itself, no explicit
- time-reversing is needed for the preparation of the adjoint sources, i.e.,
- the adjoint sources are in the same forward time sense as the original
- recorded seismograms.
-
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Set the related parameters and run the adjoint simulation
-\series default
-
-\newline
-In the
-\family typewriter
-DATA/Par_file
-\family default
-, set the two related parameters to be
-\family typewriter
-SIMULATION_TYPE = 2
-\family default
- and
-\family typewriter
-SAVE_FORWARD = .false.
-\family default
-.
- More conveniently, use the scripts
-\family typewriter
-UTILS/change_simulation_type.pl
-\family default
- to modify the
-\family typewriter
-Par_file
-\family default
- automatically (
-\family typewriter
-change_simulation_type.pl -a
-\family default
-).
- Then run the solver to launch the adjoint simulation.
-\end_layout
-
-\begin_layout Enumerate
-
-\series bold
-Collect the seismograms at the original source location
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-After the adjoint simulation has completed successfully, get the seismograms
- from directory
-\family typewriter
-OUTPUT_FILES
-\family default
-.
-
-\end_layout
-
-\begin_layout Itemize
-These adjoint seismograms are recorded at the locations of the original
- earthquake sources given by the
-\family typewriter
-DATA/CMTSOLUTION
-\family default
- file, and have names of the form
-\family typewriter
-S?????.NT.S??.sem
-\family default
- for the six-component strain tensor (
-\family typewriter
-SNN,SEE,SZZ,SNE,SNZ,SEZ
-\family default
-) at these locations, and
-\family typewriter
-S?????.NT.LH?.sem
-\family default
- for the three-component displacements (
-\family typewriter
-LHN,LHE,LHZ
-\family default
-) recorded at these locations.
-
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-S?????
-\family default
- denotes the source number; for example, if the original
-\family typewriter
-CMTSOLUTION
-\family default
- provides only a point source, then the seismograms collected will start
- with
-\family typewriter
-S00001
-\family default
-.
-
-\end_layout
-
-\begin_layout Itemize
-These adjoint seismograms provide critical information for the computation
- of the gradient of the misfit function.
-\end_layout
-
-\end_deeper
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Adjoint-simulation-finite"
-
-\end_inset
-
-Adjoint Simulations for Finite-Frequency Kernels (Kernel Simulation)
-\end_layout
-
-\begin_layout Standard
-Finite-frequency sensitivity kernels are computed in two successive simulations
- (please refer to
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{LiTr06}
-\end_layout
-
-\end_inset
-
- for details).
-\end_layout
-
-\begin_layout Enumerate
-
-\series bold
-Run a forward simulation with the state variables saved at the end of the
- simulation
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-Prepare the
-\family typewriter
-\size small
-CMTSOLUTION
-\family default
-\size default
- and
-\family typewriter
-\size small
-STATIONS
-\family default
-\size default
- files, set the parameters
-\family typewriter
-\size small
-SIMULATION_TYPE
-\family default
-
-\family typewriter
-=
-\family default
-
-\family typewriter
-1
-\family default
-\size default
- and
-\family typewriter
-\size small
-SAVE_FORWARD =
-\family default
-
-\family typewriter
-.true.
-
-\family default
-\size default
- in the
-\family typewriter
-Par_file
-\family default
- (
-\family typewriter
-change_simulation_type -F
-\family default
-), and run the solver.
-
-\end_layout
-
-\begin_layout Itemize
-Notice that attenuation is not implemented yet for the computation of finite-fre
-quency kernels; therefore set
-\family typewriter
-ATTENUATION = .false.
-
-\family default
- in the
-\family typewriter
-Par_file
-\family default
-.
-
-\end_layout
-
-\begin_layout Itemize
-We also suggest you modify the half duration of the
-\family typewriter
-CMTSOLUTION
-\family default
- to be similar to the accuracy of the simulation (see Equation
-\begin_inset LatexCommand ref
-reference "eq:shortest_period"
-
-\end_inset
-
- or
-\begin_inset LatexCommand ref
-reference "eq:shortest_period_regional"
-
-\end_inset
-
-) to avoid too much high-frequency noise in the forward wavefield, although
- theoretically the high-frequency noise should be eliminated when convolved
- with an adjoint wavefield with the proper frequency content.
-
-\end_layout
-
-\begin_layout Itemize
-This forward simulation differs from the regular simulations (
-\family typewriter
-\size small
-SIMULATION_TYPE
-\family default
-
-\family typewriter
-=
-\family default
-
-\family typewriter
-1
-\family default
-\size default
- and
-\family typewriter
-\size small
-SAVE_FORWARD
-\family default
-
-\family typewriter
-=
-\family default
-
-\family typewriter
-.false.
-\family default
-\size default
-) described in the previous chapters in that the state variables for the
- last time step of the simulation, including wavefields of the displacement,
- velocity, acceleration, etc., are saved to the
-\family typewriter
-LOCAL_PATH
-\family default
- to be used for the subsequent simulation.
-
-\end_layout
-
-\begin_layout Itemize
-For regional simulations, the files recording the absorbing boundary contributio
-n are also written to the
-\family typewriter
-LOCAL_PATH
-\family default
- when
-\family typewriter
-SAVE_FORWARD = .true.
-\family default
-.
-
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Prepare the adjoint sources
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-The adjoint sources need to be prepared the same way as described in Section\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Adjoint-simulation-sources"
-
-\end_inset
-
-, item\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "enu:Prepare-the-adjoint"
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Itemize
-In the case of travel-time finite-frequency kernel for one source-receiver
- pair, i.e., point source from the
-\family typewriter
-CMTSOLUTION
-\family default
-, and one station in the
-\family typewriter
-STATIONS_ADJOINT
-\family default
- list, we supply a sample program in
-\family typewriter
-UTILS/cut_velocity
-\family default
- to cut a certain portion of the original displacement seismograms and convert
- them into the proper adjoint source to compute the finite-frequency kernel.
-
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-cut_velocity t1 t2 ifile[0-5] E/N/Z-ascii-files [baz]
-\end_layout
-
-\begin_layout Standard
-where
-\family typewriter
-t1
-\family default
- and
-\family typewriter
-t2
-\family default
- are the start and end time of the portion you are interested in,
-\family typewriter
-ifile
-\family default
- denotes the component of the seismograms to be used (0 for all three components
-, 1 for east, 2 for north, and 3 for vertical, 4 for transverse, and 5 for
- radial component),
-\family typewriter
-E/N/Z-ascii-files
-\family default
- indicate the three-component displacement seismograms in the right order,
- and
-\family typewriter
-baz
-\family default
- is the back-azimuth of the station from the event location.
- Note that
-\family typewriter
-baz
-\family default
- is only supplied when
-\family typewriter
-ifile
-\family default
- = 4 or 5.
-\end_layout
-
-\end_deeper
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Run the kernel simulation
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-With the successful forward simulation and the adjoint source ready in
-\family typewriter
-SEM/
-\family default
-, set
-\family typewriter
-SIMULATION_TYPE = 3
-\family default
- and
-\family typewriter
-SAVE_FORWARD = .false.
-
-\family default
- in the
-\family typewriter
-Par_file(change_simulation_type.pl -b)
-\family default
-, and rerun the solver.
-
-\end_layout
-
-\begin_layout Itemize
-The adjoint simulation is launched together with the back reconstruction
- of the original forward wavefield from the state variables saved from the
- previous forward simulation, and the finite-frequency kernels are computed
- by the interaction of the reconstructed forward wavefield and the adjoint
- wavefield.
-
-\end_layout
-
-\begin_layout Itemize
-The back-reconstructed seismograms at the original station locations are
- saved to the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory at the end of the kernel simulations.
-\end_layout
-
-\begin_layout Itemize
-These back-constructed seismograms can be compared with the time-reversed
- original seismograms to assess the accuracy of the backward reconstruction,
- and they should match very well (in the time-reversed sense).
-
-\end_layout
-
-\begin_layout Itemize
-The files containing the density, P-wave speed and S-wave speed kernels
- are saved in the
-\family typewriter
-LOCAL_PATH
-\family default
- with the names of
-\family typewriter
-proc??????_reg_?_rho(alpha,beta)_kernel.bin
-\family default
-, where
-\family typewriter
-proc??????
-\family default
- represents the processor number, and
-\family typewriter
-reg_?
-\family default
- denotes the region these kernels are for, including mantle (
-\family typewriter
-reg_1
-\family default
-), outer core (
-\family typewriter
-reg_2
-\family default
-), and inner core (
-\family typewriter
-reg_3
-\family default
-).
- The output kernels are in the unit of
-\begin_inset Formula $s/km^{3}$
-\end_inset
-
-.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Run the boundary kernel simulation
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-\noindent
-If you set the
-\family typewriter
-SAVE_BOUNDARY_MESH = .true.
-
-\family default
- in the
-\family typewriter
-constants.h
-\family default
- file before the simulations, i.e., at the beginning of step 1, you will get
- not only the volumetric kernels as described in step 3, but also boundary
- kernels for the Earth's internal discontinuities, such as Moho, 410-km
- discontinuity, 670-km discontinuity, CMB and ICB.
- These kernel files are also saved in the local scratch directory defined
- by
-\family typewriter
-LOCAL_PATH
-\family default
-and have names such as
-\family typewriter
-proc??????_reg_1(2)_Moho(d400,d670,CMB,ICB)_kernel.bin
-\family default
-.
- For a theoretical derivation of the boundary kernels, refer to
-\begin_inset LatexCommand citet
-key "trompetal2005"
-
-\end_inset
-
-, and for the visualization of the boundary kernels, refer to Section
-\begin_inset LatexCommand ref
-reference "sec:Finite-Frequency-Kernels"
-
-\end_inset
-
-.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Run the anisotropic kernel simulation
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-Instead of the kernels for the isotropic wave speeds, you can also compute
- the kernels for the 21 independent components
-\begin_inset Formula $C_{IJ},\, I,J=1,...,6$
-\end_inset
-
- (using Voigt's notation) of the elastic tensor in the (spherical) geographical
- coordinate system.
- This is done by setting
-\family typewriter
-ANISOTROPIC_KL
-\family default
-
-\family typewriter
-=
-\family default
-
-\family typewriter
-.true.
-
-\family default
- in
-\family typewriter
-constants.h
-\family default
- before step 3.
- The definition of the parameters
-\begin_inset Formula $C_{IJ}$
-\end_inset
-
- in terms of the corresponding components
-\begin_inset Formula $c_{ijkl},ijkl,i,j,k,l=1,2,3$
-\end_inset
-
- of the elastic tensor in spherical coordinates follows
-\begin_inset LatexCommand citet
-key "ChTr07"
-
-\end_inset
-
-.
- The computation of the anisotropic kernels is only implemented in the crust
- and mantle regions.
- The 21 anisotropic kernels are saved in the
-\family typewriter
-LOCAL_PATH
-\family default
- in one file with the name of
-\family typewriter
-proc??????_reg1_cijkl_kernel.bin
-\family default
- (with
-\family typewriter
-proc??????
-\family default
- the processor number).
- The output kernels correspond to perturbation
-\begin_inset Formula $\delta C_{IJ}$
-\end_inset
-
- of the elastic parameters and their unit is in
-\begin_inset Formula $s/GPa/km^{3}$
-\end_inset
-
-.
- For consistency, the output density kernels with this option turned on
- are for a perturbation
-\begin_inset Formula $\delta\rho$
-\end_inset
-
- (and not
-\begin_inset Formula $\frac{\delta\rho}{\rho}$
-\end_inset
-
-) and their unit is in s / (kg/m
-\begin_inset Formula $^{3}$
-\end_inset
-
-) / km
-\begin_inset Formula $^{3}$
-\end_inset
-
-.
- These `primary' anisotropic kernels can then be combined to obtain the
- kernels related to other descriptions of anisotropy.
- This can be done, for example, when combining the kernel files from slices
- into one mesh file (see Section\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Finite-Frequency-Kernels"
-
-\end_inset
-
-).
-
-\end_layout
-
-\end_deeper
-\begin_layout Standard
-In general, the first three steps need to be run sequentially to ensure
- proper access to the necessary files at different stages.
- If the simulations are run through some cluster scheduling system (e.g.,
- LSF), and the forward simulation and the subsequent kernel simulations
- cannot be assigned to the same set of computer nodes, the kernel simulation
- will not be able to access the database files saved by the forward simulation.
- Solutions for this problem are provided in Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Running-Scheduler"
-
-\end_inset
-
-.
- Visualization of the finite-frequency kernels is discussed in Section\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Finite-Frequency-Kernels"
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Chapter
-Graphics
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Meshes"
-
-\end_inset
-
-Meshes
-\end_layout
-
-\begin_layout Standard
-Use the serial code
-\family typewriter
-combine_AVS_DX.f90
-\family default
- (type `
-\family typewriter
-make combine_AVS_DX
-\family default
-' and then `
-\family typewriter
-xcombine_AVS_DX
-\family default
-') to generate
-\begin_inset LatexCommand htmlurl
-name "AVS"
-target "www.avs.com"
-
-\end_inset
-
- output files (in AVS UCD format) or
-\begin_inset LatexCommand htmlurl
-name "OpenDX"
-target "www.opendx.org"
-
-\end_inset
-
- output files showing the mesh, the MPI partition (slices), the
-\begin_inset Formula $\nchunks$
-\end_inset
-
- chunks, the source and receiver location, etc.
- Use the AVS UCD files
-\family typewriter
-AVS_continent_boundaries.inp
-\family default
- and
-\family typewriter
-AVS_plate_boundaries.inp
-\family default
- or the OpenDX files
-\family typewriter
-DX_continent_boundaries.dx
-\family default
- and
-\family typewriter
-DX_plate_boundaries.dx
-\family default
- (that can be created using Perl scripts located in
-\family typewriter
-DATA/UTILS/opendx_AVS
-\family default
-) for reference.
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Movies"
-
-\end_inset
-
-Movies
-\end_layout
-
-\begin_layout Standard
-To make a surface or volume movie of the simulation, set parameters
-\family typewriter
-MOVIE_SURFACE
-\family default
-,
-\family typewriter
-MOVIE_VOLUME
-\family default
-, and
-\family typewriter
-NTSTEP_BETWEEN_FRAMES
-\family default
- in the
-\family typewriter
-Par_file
-\family default
-.
- Turning on the movie flags, in particular
-\family typewriter
-MOVIE_VOLUME
-\family default
-, produces large output files.
-
-\family typewriter
-MOVIE_VOLUME
-\family default
- files are saved in the
-\family typewriter
-LOCAL_PATH
-\family default
- directory, whereas
-\family typewriter
-MOVIE_SURFACE
-\family default
- output files are saved in the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory.
- We save the velocity field.
- The look of a movie is determined by the half-duration of the source.
- The half-duration should be large enough so that the movie does not contain
- frequencies that are not resolved by the mesh, i.e., it should not contain
- numerical noise.
- This can be accomplished by selecting a CMT
-\family typewriter
-HALF_DURATION
-\family default
- > 1.1
-\begin_inset Formula $\times$
-\end_inset
-
- smallest period (see figure
-\begin_inset LatexCommand ref
-reference "fig:CMTSOLUTION-file"
-
-\end_inset
-
-).
- When
-\family typewriter
-\size small
-MOVIE_SURFACE
-\family default
-\size default
- =
-\family typewriter
-\size small
-.true.
-
-\family default
-\size default
- or
-\family typewriter
-\size small
-MOVIE_VOLUME
-\family default
-
-\family typewriter
-=
-\family default
-
-\family typewriter
-.true.
-\family default
-\size default
-, the half duration of each source in the
-\family typewriter
-CMTSOLUTION
-\family default
- file is replaced by
-\end_layout
-
-\begin_layout Quote
-\begin_inset Formula \[
-\sqrt{(}\mathrm{\mathtt{HALF\_DURATIO}\mathtt{N}^{2}}+\mathrm{\mathtt{HDUR\_MOVI}\mathtt{E}^{2}})\]
-
-\end_inset
-
-
-\series bold
-NOTE:
-\series default
- If
-\family typewriter
-HDUR_MOVIE
-\family default
- is set to 0.0, the code will select the appropriate value of 1.1
-\begin_inset Formula $\times$
-\end_inset
-
- smallest period.
- As usual, for a point source one can set
-\family typewriter
-HALF_DURATION
-\family default
- in the
-\family typewriter
-Par_file
-\family default
- to be 0.0 and
-\family typewriter
-HDUR_MOVIE
-\family default
- = 0.0 to get the highest frequencies resolved by the simulation, but for
- a finite source one would keep all the
-\family typewriter
-HALF_DURATION
-\family default
-s as prescribed by the finite source model and set
-\family typewriter
-HDUR_MOVIE
-\family default
- = 0.0.
-\end_layout
-
-\begin_layout Subsection
-Movie Surface
-\end_layout
-
-\begin_layout Standard
-When running
-\family typewriter
-xspecfem3D
-\family default
- with the
-\family typewriter
-MOVIE_SURFACE
-\family default
- flag turned on the code outputs
-\family typewriter
-moviedata??????
-\family default
- files in the
-\family typewriter
-OUTPUT_FILES
-\family default
- directory.
- The files are in a fairly complicated binary format, but there are two
- programs provided to convert the output into more user friendly formats.
- The first one,
-\family typewriter
-create_movie_AVS_DX.f90
-\family default
- outputs data in ASCII, OpenDX, AVS, or ParaView format.
- Run the code from the source directory (type `
-\family typewriter
-make
-\family default
-
-\family typewriter
-create_movie_AVS_DX
-\family default
-' first) to create an input file in your format of choice.
- The code will prompt the user for input parameters.
- The second program
-\family typewriter
-create_movie_GMT_global.f90
-\family default
- outputs ASCII xyz files, convenient for use with GMT.
- This codes uses significantly less memory than
-\family typewriter
-create_movie_AVS_DX.f90
-\family default
- and is therefore useful for high resolution runs.
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/geo-poster4_small.eps
- lyxscale 75
- scale 75
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\noindent
-Snapshots from a global movie for the December 26, 2004, M=9.2 Sumatra-Andaman
- earthquake.
- Time runs down successive columns.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-\begin_inset LatexCommand label
-name "sub:Movie-Volume"
-
-\end_inset
-
-Movie Volume
-\end_layout
-
-\begin_layout Standard
-When running xspecfem3D with the
-\family typewriter
-\size small
-MOVIE_VOLUME
-\family default
-\size default
- flag turned on, the code outputs several files in
-\family typewriter
-\size small
-LOCAL_DIR
-\family default
-\size default
-.
- As the files can be very large, there are several flags in the
-\family typewriter
-\size small
-Par_file
-\family default
-\size default
- that control the region in space and time that is saved.
- These are:
-\family typewriter
-\size small
-MOVIE_TOP_KM
-\family default
-\size default
-,
-\family typewriter
-\size small
-MOVIE_BOTTOM_KM
-\family default
-\size default
-,
-\family typewriter
-\size small
-MOVIE_WEST_DEG
-\family default
-\size default
-,
-\family typewriter
-\size small
-MOVIE_EAST_DEG
-\family default
-\size default
-,
-\family typewriter
-\size small
-MOVIE_NORTH_DEG
-\family default
-\size default
-,
-\family typewriter
-\size small
-MOVIE_SOUTH_DEG
-\family default
-\size default
-,
-\family typewriter
-\size small
-MOVIE_START
-\family default
-\size default
- and
-\family typewriter
-\size small
-MOVIE_STOP
-\family default
-\size default
-.
- The code will save a given element if the center of the element is in the
- prescribed volume.
-
-\end_layout
-
-\begin_layout Description
-The\InsetSpace ~
-Top/Bottom: Depth below the surface in kilometers, use
-\family typewriter
-\size small
-MOVIE_TOP
-\family default
-\size default
-
-\family typewriter
-\size small
-=
-\family default
-\size default
-
-\family typewriter
-\size small
--100.0
-\family default
-\size default
- to make sure the surface is stored.
-
-\end_layout
-
-\begin_layout Description
-West/East: Longitude, degrees East [-180.0/180.0]
-\end_layout
-
-\begin_layout Description
-North/South: Latitute, degrees North [-90.0/90.0]
-\end_layout
-
-\begin_layout Description
-Start/Stop: Frames will be stored at
-\family typewriter
-\size small
-MOVIE_START
-\family default
-\size default
-
-\family typewriter
-\size small
-+
-\family default
-\size default
-
-\family typewriter
-\size small
-i*NSTEP_BETWEEN_FRAMES
-\family default
-\size default
-, where
-\family typewriter
-\size small
-i=(0,1,2..)
-\family default
-\size default
- while
-\family typewriter
-\size small
-i*NSTEP_BETWEEN_FRAMES
-\family default
-\size default
-
-\family typewriter
-\size small
-<=
-\family default
-\size default
-
-\family typewriter
-\size small
-MOVIE_STOP
-\end_layout
-
-\begin_layout Standard
-The code saves several files, and the output is saved by each processor.
- The first is
-\family typewriter
-\size small
-proc??????_movie3D_info.txt
-\family default
-\size default
- which contains two numbers, first the number of points within the prescribed
- volume within this particular slice, and second the number of elements.
- The next files are
-\family typewriter
-\size small
-proc??????_movie3D_x.bin
-\family default
-\size default
-,
-\family typewriter
-\size small
-proc??????_movie3D_y.bin
-\family default
-\size default
-,
-\family typewriter
-\size small
-proc??????_movie3D_z.bin
-\family default
-\size default
- which store the locations of the points in the 3D mesh.
-\end_layout
-
-\begin_layout Standard
-Finally the code stores the ``value'' at each of the points.
- Which value is determined by
-\family typewriter
-\size small
-MOVIE_VOLUME_TYPE
-\family default
-\size default
- in the
-\family typewriter
-\size small
-Par_file
-\family default
-\size default
-.
- Choose 1 to save the strain, 2 to save the time integral of strain, and
- 3 to save
-\begin_inset Formula $\mu$
-\end_inset
-
-*time integral of strain in the subvolume.
- Choosing 4 causes the code to save the trace of the stress and the deviatoric
- stress in the whole volume (not the subvolume in space), at the time steps
- specified.
- The name of the output file will depend on the
-\family typewriter
-\size small
-MOVIE_VOLUME_TYPE
-\family default
-\size default
- chosen.
-\end_layout
-
-\begin_layout Standard
-Setting
-\family typewriter
-\size small
-MOVIE_VOLUME_COARSE
-\family default
-\size default
-
-\family typewriter
-\size small
-=
-\family default
-\size default
-
-\family typewriter
-\size small
-.true.
-
-\family default
-\size default
- will make the code save only the corners of the elements, not all the points
- within each element for
-\family typewriter
-\size small
-MOVIE_VOLUME_TYPE
-\family default
-\size default
-
-\family typewriter
-\size small
-=
-\family default
-\size default
-
-\family typewriter
-\size small
-1,2,3
-\family default
-\size default
-.
-\end_layout
-
-\begin_layout Standard
-To make the code output your favorite ``value'' simply add a new
-\family typewriter
-\size small
-MOVIE_VOLUME_TYPE
-\family default
-\size default
-, a new subroutine to
-\family typewriter
-\size small
-write_movie_volume.f90
-\family default
-\size default
- and a subroutine call to
-\family typewriter
-\size small
-specfem3D.f90
-\family default
-\size default
-.
-\end_layout
-
-\begin_layout Standard
-A utility program to combine the files produced by
-\family typewriter
-\size small
-MOVIE_VOLUME_TYPE
-\family default
-\size default
-
-\family typewriter
-\size small
-=
-\family default
-\size default
-
-\family typewriter
-\size small
-1,2,3
-\family default
-\size default
- is provided in
-\family typewriter
-\size small
-combine_paraview
-\newline
-_strain_data.f90
-\family default
-\size default
-.
- Type
-\family typewriter
-\size small
-xcombine_paraview_strain_data
-\family default
-\size default
- to get the usage statement.
- The program
-\family typewriter
-\size small
-combine_vol
-\newline
-_data.f90
-\family default
-\size default
- can be used for
-\family typewriter
-\size small
-MOVIE_VOLUME_TYPE
-\family default
-\size default
-
-\family typewriter
-\size small
-=
-\family default
-\size default
-
-\family typewriter
-\size small
-4
-\family default
-\size default
-.
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Finite-Frequency-Kernels"
-
-\end_inset
-
-Finite-Frequency Kernels
-\end_layout
-
-\begin_layout Standard
-The finite-frequency kernels computed as explained in Section
-\begin_inset LatexCommand ref
-reference "sec:Adjoint-simulation-finite"
-
-\end_inset
-
- are saved in the
-\family typewriter
-LOCAL_PATH
-\family default
- at the end of the simulation.
- Therefore, we first need to collect these files on the front end, combine
- them into one mesh file, and visualize them with some auxilliary programs.
-\end_layout
-
-\begin_layout Enumerate
-
-\series bold
-Create slice files
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-We will only discuss the case of one source-receiver pair, i.e., the so-called
- banana-doughnut kernels.
- Although it is possible to collect the kernel files from all slices onto
- the front end, it usually takes up too much storage space (at least tens
- of gigabytes).
- Since the sensitivity kernels are the strongest along the source-receiver
- great circle path, it is sufficient to collect only the slices that are
- along or close to the great circle path.
-
-\end_layout
-
-\begin_layout Standard
-A Perl script
-\family typewriter
-UTILS/Paraview/global_slice_number.pl
-\family default
- 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.
-
-\end_layout
-
-\begin_layout Enumerate
-You need to first compile the utility programs provided in the
-\family typewriter
-UTILS/Paraview/global_slice_util
-\family default
-directory.
- Then copy the
-\family typewriter
-CMTSOLUTION
-\family default
- file,
-\family typewriter
-STATIONS_ADJOINT
-\family default
-, and
-\family typewriter
-Par_file
-\family default
-, and run:
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-
-\family typewriter
-global_slice_number.pl CMTSOLUTION STATIONS_ADJOINT Par_file
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-In the case of visualization boundary kernels or spherical cross-sections
- of the volumetric kernels, it is necessary to obtain the slice numbers
- that cover a belt along the source and receiver great circle path, and
- you can use the hybrid version:
-\end_layout
-
-\begin_layout LyX-Code
-globe_slice_number2.pl
-\family typewriter
- CMTSOLUTION STATIONS_ADJOINT
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
- Par_file belt_width_in_degrees
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-A typical value for
-\family typewriter
-belt_width_in_degrees
-\family roman
- can be 20.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-For a full 6-chunk simulation, this script will generate the
-\family typewriter
-slice_minor
-\family default
-,
-\family typewriter
-slice_major
-\family default
-,
-\family typewriter
-slice_ic
-\family default
- files, but for a one- or two-chunk simulation, this script only generates
- the
-\family typewriter
-slice_minor
-\family default
- file.
-
-\end_layout
-
-\begin_layout Enumerate
-For cases with multiple sources and multiple receivers, you need to provide
- a slice file before proceeding to the next step.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Collect the kernel files
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-After obtaining the slice files, you can collect the corresponding kernel
- files from the given slices.
-
-\end_layout
-
-\begin_layout Enumerate
-To accomplish this, you can use or modify the scripts in
-\family typewriter
-UTILS/collect_database
-\family default
-directory:
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-
-\size small
-copy_m(oc,ic)_globe_database.pl slice_file lsf_machine_file filename [jobid]
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-for volumetric kernels, where
-\family default
-
-\family typewriter
-\size small
-lsf_machine_file
-\family roman
-\size default
- is the machine file generated by the LSF scheduler,
-\family default
-
-\family typewriter
-\size small
-filename
-\family roman
-\size default
- is the kernel name (e.g.,
-\family default
-
-\family typewriter
-\size small
-rho_kernel
-\family roman
-\size default
-,
-\family default
-
-\family typewriter
-\size small
-alpha_kernel
-\family roman
-\size default
- and
-\family default
-
-\family typewriter
-\size small
-beta_kernel
-\family roman
-\size default
-), and the optional
-\family default
-
-\family typewriter
-\size small
-jobid
-\family roman
-\size default
- is the name of the subdirectory under
-\family default
-
-\family typewriter
-\size small
-LOCAL_PATH
-\family roman
-\size default
- where all the kernel files are stored.
- For boundary kernels, you need to use
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-\size small
-copy_surf_globe_database.pl slice_file lsf_machine_file filename [jobid]
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-where the
-\family default
-filename
-\family roman
- can be
-\family default
-
-\family typewriter
-\size small
-Moho_kernel
-\family default
-\size default
-,
-\family typewriter
-\size small
-d400_kernel
-\family default
-\size default
-,
-\family typewriter
-\size small
-d670_kernel
-\family default
-\size default
-,
-\family typewriter
-\size small
-CMB_kernel
-\family default
-\size default
-
-\family roman
-and
-\family default
-
-\family typewriter
-\size small
-ICB_kernel
-\family default
-\size default
-.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-After executing this script, all the necessary mesh topology files as well
- as the kernel array files are collected to the local directory on the front
- end.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Combine kernel files into one mesh file
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-We use an auxilliary program
-\family typewriter
-combine_vol_data.f90
-\family default
- to combine the volumetric kernel files from all slices into one mesh file,
- and
-\family typewriter
-combine_surf_data.f90
-\family default
-to combine the surface kernel files.
-\end_layout
-
-\begin_layout Enumerate
-Compile it in the global code directory:
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-
-\size footnotesize
-make combine_vol_data
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-xcombine_vol_data
-\size default
-
-\size footnotesize
-slice_list
-\size default
-
-\size footnotesize
-filename
-\size default
-
-\size footnotesize
-input_dir
-\size default
-
-\size footnotesize
-output_dir
-\size default
-
-\size footnotesize
-high/low-resolution
-\size default
-
-\size footnotesize
-[region]
-\end_layout
-
-\begin_layout Standard
-
-\family roman
-where
-\family default
-
-\family typewriter
-input_dir
-\family default
-
-\family roman
-is the directory where all the individual kernel files are stored, and
-\family default
-
-\family typewriter
-output_dir
-\family default
-
-\family roman
-is where the mesh file will be written.
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-xcombine_surf_data slice_list filename surfname input_dir output_dir hi
- gh/low-resolution 2D/3D
-\end_layout
-
-\begin_layout Standard
-where
-\family typewriter
-surfname
-\family default
- should correspond to the specific kernel file name, and can be chosen from
-
-\family typewriter
-Moho
-\family default
-,
-\family typewriter
-400
-\family default
-,
-\family typewriter
-670
-\family default
-,
-\family typewriter
-CMB
-\family default
- and
-\family typewriter
-ICB
-\family default
-.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-Use 1 for a high-resolution mesh, outputting all the GLL points to the mesh
- file, or use 0 for low resolution, outputting only the corner points of
- the elements to the mesh file.
- Use 0 for 2D surface kernel files and 1 for 3D volumetric kernel files.
-\end_layout
-
-\begin_layout Enumerate
-Use region = 1 for the mantle, region =2 for the outer core, region = 3
- for the inner core, and region = 0 for all regions.
-\end_layout
-
-\begin_layout Enumerate
-The output mesh file will have the name
-\family typewriter
-reg_?_rho(alpha,beta)_kernel.mesh,
-\family default
- or
-\family typewriter
-
-\newline
-reg_?_Moho(d400,d670,CMB,ICB)_kernel.surf.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Convert mesh files into .vtu files
-\end_layout
-
-\begin_deeper
-\begin_layout Enumerate
-We next convert the
-\family typewriter
-.mesh
-\family default
- file into the VTU (Unstructured grid file) format which can be viewed in
- ParaView, for example:
-\end_layout
-
-\begin_deeper
-\begin_layout LyX-Code
-mesh2vtu.pl -i file.mesh -o file.vtu
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-Notice that this Perl script uses a program
-\family typewriter
-mesh2vtu
-\family default
- in the
-\family typewriter
-UTILS/Parview/mesh2vtu
-\family default
- directory, which further uses the
-\begin_inset LatexCommand htmlurl
-name "VTK"
-target "www.vtk.org"
-
-\end_inset
-
- run-time library for its execution.
- Therefore, make sure you have them properly set in the script.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-Copy over the source and receiver .vtk file
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-In the case of a single source and a single receiver, the simulation also
- generates the
-\family typewriter
-OUTPUT_FILES/sr.vtk
-\family default
- file to describe the source and receiver locations, which can be viewed
- in Paraview in the next step.
-
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-
-\series bold
-View the mesh in ParaView
-\end_layout
-
-\begin_deeper
-\begin_layout Standard
-Finally, we can view the mesh in
-\begin_inset LatexCommand htmlurl
-name "ParaView"
-target "www.paraview.org"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Enumerate
-Open ParaView.
-\end_layout
-
-\begin_layout Enumerate
-From the top menu,
-\family sans
-File
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
- Open data
-\family default
-, select
-\family typewriter
-file.vtu
-\family default
-, and click the
-\family sans
-Accept
-\family default
- button.
-\end_layout
-
-\begin_deeper
-\begin_layout Itemize
-If the mesh file is of moderate size, it shows up on the screen; otherwise,
- only the outline is shown.
-\end_layout
-
-\end_deeper
-\begin_layout Enumerate
-Click
-\family sans
-Display Tab
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
-Display Style
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
-Representation
-\family default
- and select
-\family sans
-wireframe of surface
-\family default
- to display it.
-
-\end_layout
-
-\begin_layout Enumerate
-To create a cross-section of the volumetric mesh, choose
-\family sans
-Filter
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
-cut
-\family default
-, and under
-\family sans
-Parameters Tab
-\family default
-, choose
-\family sans
-Cut Function
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
-plane
-\family default
-.
-
-\end_layout
-
-\begin_layout Enumerate
-Fill in center and normal information given by the standard output from
-
-\family typewriter
-global_slice_number.pl
-\family default
- script.
-
-\end_layout
-
-\begin_layout Enumerate
-To change the color scale, go to
-\family sans
-Display Tab
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
-Color
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
-Edit Color Map
-\family default
- and reselect lower and upper limits, or change the color scheme.
-\end_layout
-
-\begin_layout Enumerate
-Now load in the source and receiver location file by
-\family sans
-File
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
- Open data
-\family default
-, select
-\family typewriter
-sr.vt
-\family default
-k, and click the
-\family sans
-Accept
-\family default
- button.
- Choose
-\family sans
-Filter
-\family default
-
-\begin_inset Formula $\rightarrow$
-\end_inset
-
-
-\family sans
- Glyph
-\family default
-, and represent the points by `
-\family sans
-spheres
-\family default
-'.
-\end_layout
-
-\begin_layout Enumerate
-For more information about ParaView, see the
-\begin_inset LatexCommand htmlurl
-name "ParaView Users Guide"
-target "www.paraview.org/files/v1.6/ParaViewUsersGuide.PDF"
-
-\end_inset
-
-.
-\end_layout
-
-\end_deeper
-\begin_layout Standard
-For illustration purposes, Figure
-\begin_inset LatexCommand ref
-reference "fig:P-wave-speed-finite-frequency"
-
-\end_inset
-
- shows the P-wave speed finite-frequency kernel for a P arrival recorded
- at an epicental distance of
-\begin_inset Formula $60^{\circ}$
-\end_inset
-
- for a deep event.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\begin_inset Graphics
- filename figures/P_alpha_60d_18s.eps
- lyxscale 90
- scale 90
- clip
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:P-wave-speed-finite-frequency"
-
-\end_inset
-
-P-wave speed finite-frequency kernel for a P arrival recorded at an epicentral
- distance of
-\begin_inset Formula $60^{\circ}$
-\end_inset
-
-.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Running-Scheduler"
-
-\end_inset
-
-Running through a Scheduler
-\end_layout
-
-\begin_layout Standard
-The code is usually run on large parallel machines, often PC clusters, most
- of which use schedulers, i.e., queuing or batch management systems to manage
- the running of jobs from a large number of users.
- The following considerations need to be taken into account when running
- on a system that uses a scheduler:
-\end_layout
-
-\begin_layout Itemize
-The processors/nodes to be used for each run are assigned dynamically by
- the scheduler, based on availability.
- Therefore, in order for the mesher and the solver (or between successive
- runs of the solver) to have access to the same database files (if they
- are stored on hard drives local to the nodes on which the code is run),
- they must be launched in sequence as a single job.
-
-\end_layout
-
-\begin_layout Itemize
-On some systems, the nodes to which running jobs are assigned are not configured
- for compilation.
- It may therefore be necessary to pre-compile both the mesher and the solver.
- A small program provided in the distribution called
-\family typewriter
-\size small
-create_header_file.f90
-\family default
-\size default
- can be used to directly create
-\family typewriter
-\size small
- OUTPUT_FILES/values_from_mesher.h
-\family default
-\size default
- using the information in the
-\family typewriter
-\size small
-DATA/Par_file
-\family default
-\size default
- without having to run the mesher (type
-\family typewriter
-\size small
-`make
-\family default
-
-\family typewriter
-create_header_
-\newline
-file
-\family default
-\size default
-' to compile it and `
-\family typewriter
-\size small
-xcreate_header_file
-\family default
-\size default
-' to run it; refer to the sample scripts below).
- The solver can now be compiled as explained above.
-
-\end_layout
-
-\begin_layout Itemize
-One feature of schedulers/queuing systems is that they allow submission
- of multiple jobs in a
-\begin_inset Quotes eld
-\end_inset
-
-launch and forget
-\begin_inset Quotes erd
-\end_inset
-
- mode.
- In order to take advantage of this property, care needs to be taken that
- output and intermediate files from separate jobs do not overwrite each
- other, or otherwise interfere with other running jobs.
-
-\end_layout
-
-\begin_layout Standard
-We describe here in some detail a job submission procedure for the Caltech
- 1024-node cluster, CITerra, under the LSF scheduling system.
- We consider the submission of a regular forward simulation.
- The two main scripts are
-\family typewriter
-\size small
-run_lsf.bash
-\family default
-\size default
-, which compiles the Fortran code and submits the job to the scheduler,
- and
-\family typewriter
-\size small
-go_mesher_solver_lsf
-\newline
-.bash
-\family default
-\size default
-, which contains the instructions that make up the job itself.
- These scripts can be found in
-\family typewriter
-\size small
-UTILS/
-\family default
-\size default
- directory and can straightforwardly be modified and adapted to meet more
- specific running needs.
-
-\end_layout
-
-\begin_layout Section
-
-\family typewriter
-run_lsf.bash
-\end_layout
-
-\begin_layout Standard
-This script first sets the job queue to be `normal'.
- It then compiles the mesher and solver together, figures out the number
- of processors required for this simulation from
-\family typewriter
-DATA/Par_file
-\family default
-, and submits the LSF job.
-\end_layout
-
-\begin_layout LyX-Code
-#!/bin/bash
-\end_layout
-
-\begin_layout LyX-Code
-# use the normal queue unless otherwise directed queue="-q normal"
-\end_layout
-
-\begin_layout LyX-Code
-if [ $# -eq 1 ]; then
-\end_layout
-
-\begin_layout LyX-Code
- echo "Setting the queue to $1"
-\end_layout
-
-\begin_layout LyX-Code
- queue="-q $1"
-\end_layout
-
-\begin_layout LyX-Code
-fi
-\newline
-
-\newline
-# compile the mesher and the solver
-\end_layout
-
-\begin_layout LyX-Code
-d=`date' echo "Starting compilation $d"
-\end_layout
-
-\begin_layout LyX-Code
-make clean
-\end_layout
-
-\begin_layout LyX-Code
-make meshfem3D
-\end_layout
-
-\begin_layout LyX-Code
-make create_header_file
-\end_layout
-
-\begin_layout LyX-Code
-xcreate_header_file
-\end_layout
-
-\begin_layout LyX-Code
-make specfem3D
-\end_layout
-
-\begin_layout LyX-Code
-d=`date'
-\end_layout
-
-\begin_layout LyX-Code
-echo "Finished compilation $d"
-\newline
-
-\newline
-# compute total number of nodes needed
-\end_layout
-
-\begin_layout LyX-Code
-NPROC_XI=`grep NPROC_XI DATA/Par_file | cut -c 34- '
-\end_layout
-
-\begin_layout LyX-Code
-NPROC_ETA=`grep NPROC_ETA DATA/Par_file | cut -c 34- '
-\end_layout
-
-\begin_layout LyX-Code
-NCHUNKS=`grep NCHUNKS DATA/Par_file | cut -c 34- '
-\newline
-
-\newline
-# total number of nodes
- is the product of the values read
-\end_layout
-
-\begin_layout LyX-Code
-numnodes=$(( $NCHUNKS * $NPROC_XI * $NPROC_ETA ))
-\newline
-
-\newline
-echo "Submitting job"
-\end_layout
-
-\begin_layout LyX-Code
-bsub $queue -n $numnodes -W 60 -K <go_mesher_solver_lsf_globe.bash
-\end_layout
-
-\begin_layout Section
-
-\family typewriter
-go_mesher_solver_lsf_globe.bash
-\end_layout
-
-\begin_layout Standard
-This script describes the job itself, including setup steps that can only
- be done once the scheduler has assigned a job-ID and a set of compute nodes
- to the job, the
-\family typewriter
-run_lsf.bash
-\family default
- commands used to run the mesher and the solver, and calls to scripts that
- collect the output seismograms from the compute nodes and perform clean-up
- operations.
-\end_layout
-
-\begin_layout Enumerate
-First the script directs the scheduler to save its own output and output
- from
-\family typewriter
-stdout
-\family default
- into
-\family typewriter
-\size small
-OUTPUT_FILES/%J.o
-\family default
-\size default
-, where
-\family typewriter
-%J
-\family default
- is short-hand for the job-ID; it also tells the scheduler what version
- of
-\family typewriter
-mpich
-\family default
- to use (
-\family typewriter
-mpich_gm
-\family default
-) and how to name this job (
-\family typewriter
-go_mesher_solver_lsf
-\family default
-).
-\end_layout
-
-\begin_layout Enumerate
-The script then creates a list of the nodes allocated to this job by echoing
- the value of a dynamically set environment variable
-\family typewriter
-LSB_MCPU_HOSTS
-\family default
- and parsing the output into a one-column list using the Perl script
-\family typewriter
-UTILS/remap_lsf_machines.pl
-\family default
-.
- It then creates a set of scratch directories on these nodes (
-\family typewriter
-\size small
-/scratch/
-\newline
-$USER/DATABASES_MPI
-\family default
-\size default
-) to be used as the
-\family typewriter
-LOCAL_PATH
-\family default
- for temporary storage of the database files.
- The scratch directories are created using
-\family typewriter
-shmux
-\family default
-, a shell multiplexor that can execute the same commands on many hosts in
- parallel.
-
-\family typewriter
-shmux
-\family default
- is available from
-\begin_inset LatexCommand htmlurl
-name "Shmux"
-target "web.taranis.org/shmux/"
-
-\end_inset
-
-.
- Make sure that the
-\family typewriter
-LOCAL_PATH
-\family default
- parameter in
-\family typewriter
-DATA/Par_file
-\family default
- is also set properly.
-\end_layout
-
-\begin_layout Enumerate
-The next portion of the script launches the mesher and then the solver using
-
-\family typewriter
-run_lsf.bash
-\family default
-.
-\end_layout
-
-\begin_layout Enumerate
-The final portion of the script performs clean up on the nodes using the
- Perl script
-\family typewriter
-cleanmulti.pl
-\end_layout
-
-\begin_layout LyX-Code
-#!/bin/bash -v
-\end_layout
-
-\begin_layout LyX-Code
-#BSUB -o OUTPUT_FILES/%J.o
-\end_layout
-
-\begin_layout LyX-Code
-#BSUB -a mpich_gm
-\end_layout
-
-\begin_layout LyX-Code
-#BSUB -J go_mesher_solver_lsf
-\end_layout
-
-\begin_layout LyX-Code
-BASEMPIDIR=/scratch/$USER/DATABASES_MPI
-\end_layout
-
-\begin_layout LyX-Code
-echo "$LSB_MCPU_HOSTS" > OUTPUT_FILES/lsf_machines
-\end_layout
-
-\begin_layout LyX-Code
-echo "$LSB_JOBID" > OUTPUT_FILES/jobid
-\end_layout
-
-\begin_layout LyX-Code
-./remap_lsf_machines.pl OUTPUT_FILES/lsf_machines >OUTPUT_FILES/machines
-\end_layout
-
-\begin_layout LyX-Code
-# Modif : create a directory for this job
-\end_layout
-
-\begin_layout LyX-Code
-shmux -M50 -Sall -c "mkdir -p /scratch/$USER;
-\end_layout
-
-\begin_layout LyX-Code
-mkdir -p $BASEMPIDIR.$LSB_JOBID" - < OUTPUT_FILES/machines >/dev/null
-\end_layout
-
-\begin_layout LyX-Code
-# Set the local path in Par_file
-\end_layout
-
-\begin_layout LyX-Code
-sed -e "s:^LOCAL_PATH .*:LOCAL_PATH = $BASEMPIDIR.$LSB_JOBID:"
-\end_layout
-
-\begin_layout LyX-Code
-< DATA/Par_file > DATA/Par_file.tmp
-\end_layout
-
-\begin_layout LyX-Code
-mv DATA/Par_file.tmp DATA/Par_file
-\end_layout
-
-\begin_layout LyX-Code
-current_pwd=$PWD
-\end_layout
-
-\begin_layout LyX-Code
-mpirun.lsf --gm-no-shmem --gm-copy-env $current_pwd/xmeshfem3D
-\end_layout
-
-\begin_layout LyX-Code
-mpirun.lsf --gm-no-shmem --gm-copy-env $current_pwd/xspecfem3D
-\end_layout
-
-\begin_layout LyX-Code
-# clean up
-\end_layout
-
-\begin_layout LyX-Code
-cleanbase_jobid.pl OUTPUT_FILES/machines DATA/Par_file
-\end_layout
-
-\begin_layout Section
-
-\family typewriter
-run_lsf.kernel
-\family default
- and
-\family typewriter
-go_mesher_solver_globe.kernel
-\end_layout
-
-\begin_layout Standard
-For kernel simulations, you can use the sample run scripts
-\family typewriter
-run_lsf.kernel
-\family default
- and
-\family typewriter
-go_mesher_solver_globe
-\newline
-.kernel
-\family default
- provided in
-\family typewriter
-UTILS
-\family default
- directory, and modify the command-line arguments of
-\family typewriter
-xcut_velocity
-\family default
- in
-\family typewriter
-go_mesher_
-\newline
-solver_globe.kernel
-\family default
-according to the start and end time of the specific portion of the forward
- seismograms you are interested in.
-\end_layout
-
-\begin_layout Chapter
-
-\size normal
-\begin_inset LatexCommand label
-name "cha:-Changing-the"
-
-\end_inset
-
-
-\size default
- Changing the Model
-\end_layout
-
-\begin_layout Standard
-In this section we explain how to change the crustal, mantle, or inner core
- models.
- These changes involve contributing specific subroutines that replace existing
- subroutines in the
-\family typewriter
-SPECFEM3D_GLOBE
-\family default
- package.
-\end_layout
-
-\begin_layout Section
-
-\size normal
-\begin_inset LatexCommand label
-name "sec:Changing-the-Crustal"
-
-\end_inset
-
-
-\size default
-Changing the Crustal Model
-\end_layout
-
-\begin_layout Standard
-The 3D crustal model Crust2.0
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{BaLaMa00}
-\end_layout
-
-\end_inset
-
- is superimposed onto the mesh by the subroutine
-\family typewriter
-crustal_model
-\newline
-.f90
-\family default
-.
- To accomplish this, the flag
-\family typewriter
-CRUSTAL
-\family default
-, set in the subroutine
-\family typewriter
-read_compute_parameters.f90
-\family default
-, is used to indicate a 3D crustal model.
- When this flag is set to
-\family typewriter
-.true.
-\family default
-, the crust on top of the 1D reference model (PREM, IASP91, or AK135) is
- removed and replaced by extending the mantle.
- The 3D crustal model is subsequently overprinted onto the crust-less 1D
- reference model.
- The call to the 3D crustal routine is of the form
-\end_layout
-
-\begin_layout LyX-Code
-call crustal_model(lat,lon,r,vp,vs,rho,moho,foundcrust,CM_V)
-\end_layout
-
-\begin_layout Standard
-Input to this routine consists of:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-lat
-\family default
- Latitude in degrees.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-lon
-\family default
- Longitude in degrees.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-r
-\family default
- Non-dimensionalized radius (
-\begin_inset Formula $0<\texttt{r}<1$
-\end_inset
-
-).
-
-\end_layout
-
-\begin_layout Standard
-Output from the routine consists of:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-vp
-\family default
- Non-dimensionalized compressional wave speed at location (
-\family typewriter
-lat
-\family default
-,
-\family typewriter
-lon
-\family default
-,
-\family typewriter
-r
-\family default
-).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-vs
-\family default
- Non-dimensionalized shear wave speed.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-rho
-\family default
- Non-dimensionalized density.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-moho
-\family default
- Non-dimensionalized Moho depth.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-found_crust
-\family default
- Logical that is set to
-\family typewriter
-.true.
-
-\family default
- only if crust exists at location (
-\family typewriter
-lat
-\family default
-,
-\family typewriter
-lon
-\family default
-,
-\family typewriter
-r
-\family default
-), i.e.,
-\family typewriter
-.false.
-
-\family default
- for radii
-\family typewriter
-r
-\family default
- in the mantle.
- This flags determines whether or not a particular location is in the crust
- and, if so, what parameters to assign to the mesh at this location.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-CM_V
-\family default
- Fortran structure that contains the parameters, variables and arrays that
- describe the model.
-
-\end_layout
-
-\begin_layout Standard
-All output needs to be non-dimensionalized according to the convention summarize
-d in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Non-Dimensionalization-Conventions"
-
-\end_inset
-
-.
- You can replace this subroutine by your own routine
-\shape italic
-provided you do not change the call structure of the routine
-\shape default
-, i.e., the new routine should take exactly the same input and produce the
- required, properly non-dimensionalized output.
-\end_layout
-
-\begin_layout Standard
-Part of the file
-\family typewriter
-crustal_model.f90
-\family default
- is the subroutine
-\family typewriter
-read_crustal_model
-\family default
-.
- The call to this routine takes argument
-\family typewriter
-CM_V
-\family default
- and is used to once-and-for-all read in the databases related to Crust2.0.
- If you replace the file
-\family typewriter
-crustal_model.f90
-\family default
- with your own implementation, you
-\shape italic
-must
-\shape default
- provide a
-\family typewriter
-read_crustal_model
-\family default
- routine, even if it does nothing.
- Model constants and variables read by the routine
-\family typewriter
-read_crustal_model
-\family default
- are passed to the subroutine
-\family typewriter
-read_crustal_model
-\family default
- through the structure
-\family typewriter
-CM_V
-\family default
-.
- An alternative crustal model should use the same construct.
- Please feel free to contribute subroutines for new models and send them
- to us so that they can be included in future releases of the software.
-\end_layout
-
-\begin_layout Quote
-
-\series bold
-NOTE:
-\series default
- If you decide to create your own version of file
-\family typewriter
-crustal_model.f90
-\family default
-, you must add calls to
-\family typewriter
-MPI_BCAST
-\family default
- in file
-\family typewriter
-meshfem3D.f90
-\family default
- after the call to the
-\family typewriter
-read_crustal_model
-\family default
- subroutine that reads the isotropic mantle model once and for all in the
- mesher.
- This is done in order to read the (potentially large) model data files
- on the master node (which is the processor of rank 0 in our code) only
- and then send a copy to all the other nodes using an MPI broadcast, rather
- than using an implementation in which all the nodes would read the same
- model data files from a remotely-mounted home file system, which could
- create a bottleneck on the network in the case of a large number of nodes.
- For example, in the current call to that routine from
-\family typewriter
-meshfem3D.f90,
-\family default
- we write:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-! the variables read are declared and stored in structure CM_V
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- if(myrank == 0) call read_crustal_model(CM_V)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-! broadcast the information read on the master to the nodes
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(CM_V%thlr,NKEYS_CRUST*NLAYERS_CRUST,MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(CM_V%velocp,NKEYS_CRUST*NLAYERS_CRUST,MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(CM_V%velocs,NKEYS_CRUST*NLAYERS_CRUST,MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(CM_V%dens,NKEYS_CRUST*NLAYERS_CRUST,MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(CM_V%abbreviation,NCAP_CRUST*NCAP_CRUST,MPI_CHARACTER,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(CM_V%code,2*NKEYS_CRUST,MPI_CHARACTER,0,MPI_COMM_WORLD,ier)
-
-\end_layout
-
-\begin_layout Section
-
-\size normal
-\begin_inset LatexCommand label
-name "sec:Changing-the-Mantle"
-
-\end_inset
-
-
-\size default
-Changing the Mantle Model
-\end_layout
-
-\begin_layout Standard
-This section discusses how to change isotropic and anisotropic 3D mantle
- models.
- Usually such changes go hand-in-hand with changing the 3D crustal model.
-\end_layout
-
-\begin_layout Subsection
-
-\size normal
-\begin_inset LatexCommand label
-name "sub:Isotropic-Models"
-
-\end_inset
-
-Isotropic Models
-\end_layout
-
-\begin_layout Standard
-The 3D mantle model S20RTS
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citep{RiVaWo99}
-\end_layout
-
-\end_inset
-
- is superimposed onto the mantle mesh by the subroutine
-\family typewriter
-mantle_model.f90
-\family default
-.
- The call to this subroutine is of the form
-\end_layout
-
-\begin_layout LyX-Code
-call mantle_model(radius,theta,phi,dvs,dvp,drho,D3MM_V)
-\end_layout
-
-\begin_layout Standard
-Input to this routine consists of:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-radius
-\family default
- Non-dimensionalized radius (
-\begin_inset Formula $\texttt{RCMB/R\_ EARTH}<\texttt{r}<\texttt{RMOHO/R\_ EARTH}$
-\end_inset
-
-; for a given 1D reference model, the constants
-\family typewriter
-RCMB
-\family default
- and
-\family typewriter
-RMOHO
-\family default
- are set in the
-\family typewriter
-\size small
-read_compute_parameters
-\size default
-.f90
-\family default
- file).
- The code expects the isotropic mantle model to be defined between the Moho
- (with radius
-\family typewriter
-RMOHO
-\family default
- in m) and the core-mantle boundary (CMB; radius
-\family typewriter
-RCMB
-\family default
- in m) of a 1D reference model.
- When a 3D crustal model is superimposed, as will usually be the case, the
- 3D mantle model is stretched to fill any potential gap between the radius
- of the Moho in the 1D reference model and the Moho in the 3D crustal model.
- Thus, when the Moho in the 3D crustal model is shallower than the Moho
- in the reference model, e.g., typically below the oceans, the mantle model
- is extended to fill this gap.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-theta
-\family default
- Colatitude in radians.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-phi
-\family default
- Longitude in radians.
-
-\end_layout
-
-\begin_layout Standard
-Output from the routine are the following non-dimensional perturbations:
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-dvs
-\family default
- Relative shear-wave speed perturbations
-\begin_inset Formula $\delta\beta/\beta$
-\end_inset
-
- at location (
-\family typewriter
-radius
-\family default
-,
-\family typewriter
-theta
-\family default
-,
-\family typewriter
-phi
-\family default
-).
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-dvp
-\family default
- Relative compressional-wave speed perturbations
-\begin_inset Formula $\delta\alpha/\alpha$
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-drho
-\family default
- Relative density perturbations
-\begin_inset Formula $\delta\rho/\rho$
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-D3MM_V
-\family default
- Fortran structure that contains the parameters, variables and arrays that
- describe the model.
-\end_layout
-
-\begin_layout Standard
-You can replace the
-\family typewriter
-mantle_model.f90
-\family default
- file with your own version
-\shape italic
-provided you do not change the call structure of the routine
-\shape default
-, i.e., the new routine should take exactly the same input and produce the
- required relative output.
-\end_layout
-
-\begin_layout Standard
-Part of the file
-\family typewriter
-mantle_model.f90
-\family default
- is the subroutine
-\family typewriter
-read_mantle_model
-\family default
-.
- The call to this routine takes argument
-\family typewriter
- D3MM_V
-\family default
- and is used to once-and-for-all read in the databases related to S20RTS.
- If you replace the file
-\family typewriter
-mantle_model.f90
-\family default
- with your own implementation, you
-\shape italic
-must
-\shape default
- provide a
-\family typewriter
-read_mantle_model
-\family default
- routine, even if it does nothing.
- Model constants and variables read by the routine
-\family typewriter
-read_mantle_model
-\family default
- are passed to the subroutine
-\family typewriter
-read_mantle_model
-\family default
- through the structure
-\family typewriter
-D3MM_V.
-
-\family default
- An alternative mantle model should use the same construct.
-\end_layout
-
-\begin_layout Quote
-
-\series bold
-NOTE:
-\series default
- If you decide to create your own version of file
-\family typewriter
-mantle_model.f90
-\family default
-, you must add calls to
-\family typewriter
-MPI_BCAST
-\family default
- in file
-\family typewriter
-meshfem3D.f90
-\family default
- after the call to the
-\family typewriter
-read_mantle_model
-\family default
- subroutine that reads the isotropic mantle model once and for all in the
- mesher.
- This is done in order to read the (potentially large) model data files
- on the master node (which is the processor of rank 0 in our code) only
- and then send a copy to all the other nodes using an MPI broadcast, rather
- than using an implementation in which all the nodes would read the same
- model data files from a remotely-mounted home file system, which could
- create a bottleneck on the network in the case of a large number of nodes.
- For example, in the current call to that routine from
-\family typewriter
-meshfem3D.f90,
-\family default
- we write:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-! the variables read are declared and stored in structure D3MM_V
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- if(myrank == 0) call read_mantle_model(D3MM_V)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-! broadcast the information read on the master to the nodes
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%dvs_a,(NK+1)*(NS+1)*(NS+1),MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%dvs_b,(NK+1)*(NS+1)*(NS+1),MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%dvp_a,(NK+1)*(NS+1)*(NS+1),MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%dvp_b,(NK+1)*(NS+1)*(NS+1),MPI_DOUBLE_PRECISION,
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- 0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%spknt,NK+1,MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD,ier)
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%qq0,(NK+1)*(NK+1),MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD,
-ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(D3MM_V%qq,3*(NK+1)*(NK+1),MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD
-,ier)
-\end_layout
-
-\begin_layout Subsection
-
-\size normal
-\begin_inset LatexCommand label
-name "sub:Anisotropic-Models"
-
-\end_inset
-
-Anisotropic Models
-\end_layout
-
-\begin_layout Standard
-Three-dimensional anisotropic mantle models may be superimposed on the mesh
- based upon the subroutine
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-anisotropic_mantle_model.f90
-\end_layout
-
-\begin_layout Standard
-The call to this subroutine is of the form
-\end_layout
-
-\begin_layout LyX-Code
-call anisomantlemodel(r,theta,phi,rho, &
-\end_layout
-
-\begin_layout LyX-Code
- c11,c12,c13,c14,c15,c16,c22,c23,c24,c25,c26, &
-\end_layout
-
-\begin_layout LyX-Code
- c33,c34,c35,c36,c44,c45,c46,c55,c56,c66,AMM_V)
-\end_layout
-
-\begin_layout Standard
-Input to this routine consists of:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-r
-\family default
- Non-dimensionalized radius (
-\begin_inset Formula $\texttt{RCMB/R\_ EARTH}<\texttt{r}<\texttt{RMOHO/R\_ EARTH}$
-\end_inset
-
-; for a given 1D reference model, the constants
-\family typewriter
-RCMB
-\family default
- and
-\family typewriter
-RMOHO
-\family default
- are set in the
-\family typewriter
-\size small
-read_compute_parameters
-\size default
-.f90
-\family default
- file).
- The code expects the anisotropic mantle model to be defined between the
- Moho and the core-mantle boundary (CMB).
- When a 3D crustal model is superimposed, as will usually be the case, the
- 3D mantle model is stretched to fill any potential gap between the radius
- of the Moho in the 1D reference model and the Moho in the 3D crustal model.
- Thus, when the Moho in the 3D crustal model is shallower than the Moho
- in the reference model, e.g., typically below the oceans, the mantle model
- is extended to fill this gap.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-theta
-\family default
- Colatitude in radians.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-phi
-\family default
- Longitude in radians.
-
-\end_layout
-
-\begin_layout Standard
-Output from the routine consists of the following non-dimensional model
- parameters:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-rho
-\family default
- Non-dimensionalized density
-\begin_inset Formula $\rho$
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-c11
-\family default
-,
-\series bold
-
-\begin_inset Formula $\cdots$
-\end_inset
-
-,
-\series default
-
-\family typewriter
-\series bold
-c66
-\family default
-\series default
- 21 non-dimensionalized anisotropic elastic parameters.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-AMM_V
-\family default
- Fortran structure that contains the parameters, variables and arrays that
- describe the model.
-
-\end_layout
-
-\begin_layout Standard
-You can replace the
-\family typewriter
-anisotropic_mantle_model.f90
-\family default
- file by your own version
-\shape italic
-provided you do not change the call structure of the routine
-\shape default
-, i.e., the new routine should take exactly the same input and produce the
- required relative output.
- Part of the file
-\family typewriter
-anisotropic_mantle_model.f90
-\family default
- is the subroutine
-\family typewriter
-read_aniso_mantle_model
-\family default
-.
- The call to this routine takes argument
-\family typewriter
-AMM_V
-\family default
- and is used to once-and-for-all read in the static databases related to
- the anisotropic model.
- When you choose to replace the file
-\family typewriter
-anisotropic_mantle_model.f90
-\family default
- with your own implementation you
-\shape italic
-must
-\shape default
- provide a
-\family typewriter
-read_aniso_mantle_model
-\family default
- routine, even if it does nothing.
- Model constants and variables read by the routine
-\family typewriter
-read_mantle_model
-\family default
- are passed through the structure
-\family typewriter
-AMM_V
-\family default
-.
- An alternative anisotropic mantle model should use the same construct.
-\end_layout
-
-\begin_layout Quote
-
-\series bold
-NOTE:
-\series default
- If you decide to create your own version of file
-\family typewriter
-anisotropic_mantle_model.f90
-\family default
-, you must add calls to
-\family typewriter
-MPI_BCAST
-\family default
- in file
-\family typewriter
-meshfem3D.f90
-\family default
- after the call to the
-\family typewriter
-read_aniso_mantle_model
-\family default
- subroutine that reads the anisotropic mantle model once and for all in
- the mesher.
- This is done in order to read the (potentially large) model data files
- on the master node (which is the processor of rank 0 in our code) only
- and then send a copy to all the other nodes using an MPI broadcast, rather
- than using an implementation in which all the nodes would read the same
- model data files from a remotely-mounted home file system, which could
- create a bottleneck on the network in the case of a large number of nodes.
- For example, in the current call to that routine from
-\family typewriter
-meshfem3D.f90,
-\family default
- we write:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-! the variables read are declared and stored in structure AMM_V
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- if(myrank == 0) call read_aniso_mantle_model(AMM_V)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-! broadcast the information read on the master to the nodes
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(AMM_V%npar1,1,MPI_INTEGER,0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(AMM_V%beta,14*34*37*73,MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD,ie
-r)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
- call MPI_BCAST(AMM_V%pro,47,MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD,ier)
-\end_layout
-
-\begin_layout Standard
-Rotation of the anisotropic tensor elements from one coordinate system to
- another coordinate system may be accomplished based upon the subroutine
-
-\family typewriter
-rotate_aniso_tensor
-\family default
-.
- Use of this routine requires understanding the coordinate system used in
-
-\family typewriter
-SPECFEM3D_GLOBE
-\family default
-, as discussed in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Reference-Frame-Convention"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Section
-
-\size normal
-\begin_inset LatexCommand label
-name "sec:Anelastic-Models"
-
-\end_inset
-
-
-\size default
-Anelastic Models
-\end_layout
-
-\begin_layout Standard
-Three-dimensional anelastic (attenuation) models may be superimposed onto
- the mesh based upon your subroutine
-\family typewriter
-{attenuation_model
-\family default
-}.
- The call to this routine is as follows
-\end_layout
-
-\begin_layout LyX-Code
-call attenuation_model(radius, latitude, longitude, Qmu, idoubling)
-\end_layout
-
-\begin_layout Standard
-Input to this routine consists of:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-radius
-\family default
- scaled radius of the earth:
-\begin_inset Formula $0\,(\mathrm{center})<=r\,<=1$
-\end_inset
-
-(surface)
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-latitude
-\family default
- Latitude in degrees:
-\begin_inset Formula $-90^{\circ}<=\theta<=90^{\circ}$
-\end_inset
-
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-longitude
-\family default
- Longitude in degrees:
-\begin_inset Formula $-180^{\circ}<=\phi<=180^{\circ}$
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Output to this routine consists of:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-Qmu
-\family default
- Shear wave quality factor:
-\begin_inset Formula $0<Q_{\mu}<5000$
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If run without modification, a PREM attenuation structure will be implemented,
- using the routine
-\family typewriter
-\size small
-{attenuation_model
-\newline
-_1D_PREM}
-\family default
-\size default
-, found in
-\family typewriter
-\size small
-attenuation_model.f90
-\family default
-\size default
-, within the
-\family typewriter
-\size small
-{get_model}
-\family default
-\size default
- routine.
-\end_layout
-
-\begin_layout Standard
-To create your own attenuation model, you need to modify your model using
- the
-\family typewriter
-\size small
-{attenuation_model_1D_PREM}
-\family default
-\size default
- subroutine and the example routine above as a guide.
- Replace the call to
-\family typewriter
-\size small
-{attenuation_model_1D_PREM}
-\family default
-\size default
- in
-\family typewriter
-\size small
-{get_model}
-\family default
-\size default
- to your own subroutine.
-\end_layout
-
-\begin_layout Standard
-Note that the resolution and maximum value of anelastic models are truncated.
- This speeds the construction of the standard linear solids during the meshing
- stage.
- To change the resolution, currently at one significant figure following
- the decimal, or the maximum value (5000), consult
-\family typewriter
-constants.h
-\family default
-.
- In order to prevent unexpected results, quality factors
-\begin_inset Formula $Q_{\mu}$
-\end_inset
-
- should never be equal to 0 outside of the inner core.
-
-\end_layout
-
-\begin_layout Chapter
-Post-Processing Scripts
-\end_layout
-
-\begin_layout Standard
-Several post-processing scripts/programs are provided in the
-\family typewriter
-UTILS/seis_process
-\family default
- directory, and most of them need to be adjusted when used on different
- systems, for example, the path of the executable programs.
- Here we only list the available scripts and provide a brief description,
- and you can either refer to the related sections for detailed usage or,
- in a lot of cases, type the script/program name without arguments for its
- usage.
-\end_layout
-
-\begin_layout Section
-Clean Local Database
-\end_layout
-
-\begin_layout Standard
-After all the simulations are done, you may need to clean the local 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
-\family typewriter
-UTILS/
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-cleanbase.pl machines
-\end_layout
-
-\begin_layout Section
-Process Data and Synthetics
-\begin_inset LatexCommand label
-name "sec:Process-data-and-syn"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In many cases, the SEM synthetics are calculated and compared to data seismogram
-s recorded at seismic stations.
- Since the SEM synthetics are accurate for a certain frequency range, both
- the original data and the synthetics need to be processed before a comparison
- can be made.
- We generally use the following scripts:
-\end_layout
-
-\begin_layout Subsection
-
-\family typewriter
-process_data.pl
-\end_layout
-
-\begin_layout Standard
-This script cuts a given portion of the original data, filters it, transfers
- the data into a displacement record, and picks the first P and S arrivals.
- For more functionality, type `
-\family typewriter
-process_data.pl
-\family default
-' without any argument.
- An example of the usage of the script:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-process_data.pl -m CMTSOLUTION -l 0/4000 -t 40/500 -i -p -x bp 1999.330*.LH?.SAC
-\end_layout
-
-\begin_layout Standard
-which has cut all the sac files between 0 and 4000 seconds, filtered them
- between 40 and 500 seconds, transfered them into displacement records,
- picked the first P and S arrivals, and add suffix `
-\family typewriter
-bp
-\family default
-' to the file names.
-\end_layout
-
-\begin_layout Standard
-Note that all of the scripts in this section actually use the SAC, saclst
- and/or IASP91 to do the core operations; therefore make sure that SAC,
- saclst and IASP91 packages are installed properly on your system, and that
- all the environment variables are set properly before running these scripts.
-\end_layout
-
-\begin_layout Subsection
-
-\family typewriter
-\begin_inset LatexCommand label
-name "sub:process_syn.pl"
-
-\end_inset
-
-process_syn.pl
-\end_layout
-
-\begin_layout Standard
-This script converts the synthetic output from the SEM code from ASCII to
- SAC format, and performs similar operations as `
-\family typewriter
-process_data.pl
-\family default
-'.
- An example of the usage of the script:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
-process_syn.pl -m CMTSOLUTION -h -a STATIONS -l 0/4000 -t 40/500 -p -x bp
- syn/*.LH?.semd
-\end_layout
-
-\begin_layout Standard
-which will convolve the synthetics with a triangular source-time function
- from the
-\family typewriter
-CMTSOLUTION
-\family default
- file, convert the synthetics into SAC format, add event and station information
- into the SAC headers, cut the SAC files between 0 and 4000 seconds, filter
- them between 40 and 500 seconds, pick the first P and S arrivals, and add
- the suffix `
-\family typewriter
-bp
-\family default
-' to the file names.
-\end_layout
-
-\begin_layout Standard
-More options are available for this script, such as adding time shift to
- the origin time of the synthetics, convolving the synthetics with a triangular
- source time function with a given half duration, etc.
- Type
-\family typewriter
-process_syn.pl
-\family default
- without any argument for a detailed usage.
-\end_layout
-
-\begin_layout Subsection
-
-\family typewriter
-rotate.pl
-\end_layout
-
-\begin_layout Standard
-To rotate the horizontal components of both the data and the synthetics
- (LHN and LHE) to the transverse and radial direction (LHT and LHR),
-\family typewriter
-\size small
-
-\family default
-\size default
-use
-\size small
-
-\family typewriter
-rotate.pl
-\family default
-\size default
-:
-\end_layout
-
-\begin_layout LyX-Code
-rotate.pl -l 0 -L 4000 -d DATA/*.LHE.SAC.bp
-\end_layout
-
-\begin_layout LyX-Code
-rotate.pl -l 0 -L 4000 SEM/*.LHE.semd.sac.bp
-\end_layout
-
-\begin_layout Standard
-where the first command performs rotation on the SAC data obtained through
- IRIS (which may have timing information written in the filename), while
- the second command rotates the processed synthetics.
-\end_layout
-
-\begin_layout Standard
-For synthetics, another (simpler) option is to set flag
-\family typewriter
-ROTATE_SEISMOGRAMS_RT
-\family default
- to
-\family typewriter
-.true.
-
-\family default
- in the parameter file
-\family typewriter
-DATA/Par_file
-\family default
-.
-\end_layout
-
-\begin_layout Subsection
-
-\family typewriter
-clean_sac_headers_after_crash.sh
-\end_layout
-
-\begin_layout Standard
-Note: You need to have the
-\family typewriter
-sismoutil-0.9b
-\family default
- package installed on your computer if you want to run this script on binary
- SAC files.
- The software is available at the
-\begin_inset LatexCommand htmlurl
-name "ORFEUS web site"
-target "www.orfeus-eu.org"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-In case the simulation crashes during run-time without computing and writing
- all time steps, the SAC files (if flags
-\family typewriter
-OUTPUT_SEISMOS_SAC_ALPHANUM
-\family default
- or
-\family typewriter
-OUTPUT_SEISMOS_SAC_BINARY
-\family default
- have been set to
-\family typewriter
-.true.
-\family default
-) are corrupt and cannot be used properly in SAC.
- If the simulation ran long enough so that the synthetic data may still
- be of use, you can run the script called
-\family typewriter
-clean_sac_headers_after_crash.sh
-\family default
- (located in the
-\family typewriter
-UTILS
-\family default
- directory) on the SAC files to correct the header variable NPTS to the
- actually written number of time steps.
- The script must be called from the
-\family typewriter
-SPECFEM3D
-\family default
- main directory, and the input argument to this script is simply a list
- of SAC seismogram files.
-
-\end_layout
-
-\begin_layout Section
-Map Local Database
-\end_layout
-
-\begin_layout Standard
-A sample program
-\family typewriter
-remap_database
-\family default
- is provided to map the local database from a set of machines to another
- set of machines.
- This is especially useful when you want to run mesher and solver, or different
- types of solvers separately through a scheduler (refer to Chapter\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "cha:Running-Scheduler"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout LyX-Code
-run_lsf.bash --gm-no-shmem --gm-copy-env remap_database
-\end_layout
-
-\begin_layout LyX-Code
-old_machines 150 [old_jobid new_jobid]
-\end_layout
-
-\begin_layout Standard
-where
-\family typewriter
-old_machines
-\family default
- is the LSF machine file used in the previous simulation, and
-\family typewriter
-150
-\family default
- is the number of processors in total.
- Note that you need to supply
-\family typewriter
-old_jobid
-\family default
- and
-\family typewriter
-new_jobid(%J)
-\family default
- which are the LSF job-IDs for the old and new run if your databases are
- stored in a sub-directory named after the jobid on the scratch disk.
-\end_layout
-
-\begin_layout Chapter*
-\begin_inset LatexCommand label
-name "cha:Bug-Reports-and"
-
-\end_inset
-
-Bug Reports and Suggestions for Improvements
-\end_layout
-
-\begin_layout Standard
-To report bugs or suggest improvements to the code, please send an e-mail
- to the
-\begin_inset LatexCommand url
-name "CIG Computational Seismology Mailing List"
-target "cig-seismo at geodynamics.org"
-
-\end_inset
-
- or
-\begin_inset LatexCommand url
-name "Jeroen Tromp"
-target "jtromp-AT-gps.caltech.edu"
-
-\end_inset
-
-, and/or use our online bug tracking system
-\begin_inset LatexCommand htmlurl
-name "Roundup"
-target "www.geodynamics.org/roundup"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Chapter*
-\begin_inset LatexCommand label
-name "cha:Notes-and-Acknowledgements"
-
-\end_inset
-
-Notes and Acknowledgements
-\end_layout
-
-\begin_layout Standard
-In order to keep the software package thread-safe in case a multithreaded
- implementation of MPI is used, developers should not add modules or common
- blocks to the source code but rather use regular subroutine arguments (which
- can be grouped in ``derived types'' if needed for clarity).
-\end_layout
-
-\begin_layout Standard
-The Gauss-Lobatto-Legendre subroutines in
-\family typewriter
-gll_library.f90
-\family default
- are based in part on software libraries from the Massachusetts Institute
- of Technology, Department of Mechanical Engineering (Cambridge, Massachusetts).
- The non-structured global numbering software was provided by Paul F.
- Fischer (Brown University, Providence, Rhode Island).
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand htmlurl
-name "OpenDX"
-target "www.opendx.org"
-
-\end_inset
-
- is open-source based on IBM Data Explorer,
-\begin_inset LatexCommand htmlurl
-name "AVS"
-target "www.avs.com"
-
-\end_inset
-
- is a trademark of Advanced Visualization Systems, and
-\begin_inset LatexCommand htmlurl
-name "ParaView"
-target "www.paraview.com"
-
-\end_inset
-
- is an open-source visualization platform.
-
-\size small
-
-\end_layout
-
-\begin_layout Standard
-The main developers of the
-\family typewriter
-SPECFEM3D_GLOBE
-\family default
- source code are Dimitri Komatitsch, Jeroen Tromp, Qinya Liu and David Michéa.
- The following individuals (listed in alphabetical order) have also contributed
- to the development of the source code: Min Chen, Vala Hjörleifsdóttir,
- Nicolas Le Goff, Brian Savage, Bernhard Schuberth, Anne Sieminski, Leif
- Strand and Peter van Keken.
- The following individuals (listed in alphabetical order) contributed to
- this manual: Min Chen, Vala Hjörleifsdóttir, Sue Kientz, Dimitri Komatitsch,
- Qinya Liu, Alessia Maggi, David Michéa, Brian Savage, Anne Sieminski, Carl
- Tape, and Jeroen Tromp.
- The manual's cover graphic was created by Santiago Lombeyda from Caltech's
-
-\begin_inset LatexCommand htmlurl
-name "Center for Advanced Computing Research (CACR)"
-target "http://www.cacr.caltech.edu/"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-Please e-mail your feedback, questions, comments, and suggestions to
-\begin_inset LatexCommand url
-name "Jeroen Tromp"
-target "jtromp-AT-gps.caltech.edu"
-
-\end_inset
-
- or to the
-\begin_inset LatexCommand url
-name "CIG Computational Seismology Mailing List"
-target "cig-seismo at geodynamics.org"
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Chapter*
-\begin_inset LatexCommand label
-name "cha:Copyright"
-
-\end_inset
-
-Copyright
-\end_layout
-
-\begin_layout Standard
-Main authors: Dimitri Komatitsch and Jeroen Tromp
-\end_layout
-
-\begin_layout Standard
-Seismological Laboratory, California Institute of Technology, U.S., and University
- of Pau / CNRS / INRIA, France
-\end_layout
-
-\begin_layout Standard
-© California Institute of Technology and University of Pau / CNRS / INRIA,
- February 2008
-\end_layout
-
-\begin_layout Standard
-This program is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the Free
- Software Foundation (see Appendix
-\begin_inset LatexCommand ref
-reference "cha:License"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-
-\size small
-\begin_inset LatexCommand bibtex
-bibfiles "bibliography"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Chapter
-\start_of_appendix
-\begin_inset LatexCommand label
-name "cha:Reference-Frame-Convention"
-
-\end_inset
-
-Reference Frame Convention
-\end_layout
-
-\begin_layout Standard
-The code uses the following convention for the Cartesian reference frame:
-
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $x$
-\end_inset
-
- axis points East
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $y$
-\end_inset
-
- axis points North
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $z$
-\end_inset
-
- axis points up
-\end_layout
-
-\begin_layout Standard
-Note that this convention is different from both the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-citet{AkRi80}
-\end_layout
-
-\end_inset
-
- convention and the Harvard Centroid-Moment Tensor (CMT) convention.
- The Aki & Richards convention is
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $x$
-\end_inset
-
- axis points North
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $y$
-\end_inset
-
- axis points East
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $z$
-\end_inset
-
- axis points down
-\end_layout
-
-\begin_layout Standard
-and the Harvard CMT convention is
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $x$
-\end_inset
-
- axis points South
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $y$
-\end_inset
-
- axis points East
-\end_layout
-
-\begin_layout Itemize
-the
-\begin_inset Formula $z$
-\end_inset
-
- axis points up
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:Non-Dimensionalization-Conventions"
-
-\end_inset
-
-Non-Dimensionalization Conventions
-\size small
-
-\end_layout
-
-\begin_layout Standard
-All physical parameters used by the code are non-dimensionalized according
- to the conventions summarized in Table\InsetSpace ~
-
-\size small
-
-\begin_inset LatexCommand ref
-reference "table:conventions"
-
-\end_inset
-
-.
-
-\begin_inset Float table
-placement ht
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-
-\size small
-\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="2">
-<features>
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
-<column alignment="center" valignment="top" rightline="true" width="0">
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-quantity (units)
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-non-dimensionalized with
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-distance (m)
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-
-\family typewriter
-R_EARTH
-\family default
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-time (s)
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-\begin_inset Formula $\sqrt{\texttt{PI}\times\texttt{GRAV}\times\texttt{RHOAV}}$
-\end_inset
-
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-density (kg/m
-\begin_inset Formula $^{3}$
-\end_inset
-
-)
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" bottomline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-
-\family typewriter
-RHOAV
-\family default
-
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Non-dimensionalization employed by the code.
- The constants
-\family typewriter
-R_EARTH
-\family default
- (the radius of the Earth),
-\family typewriter
-PI
-\family default
- (the number
-\begin_inset Formula $\pi$
-\end_inset
-
-),
-\family typewriter
-GRAV
-\family default
- (the universal gravitational constant), and
-\family typewriter
-RHOAV
-\family default
- (the Earth's average density) are defined in the
-\family typewriter
-constants.h
-\family default
- file.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\size small
-\begin_inset LatexCommand label
-name "table:conventions"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Chapter
-Benchmarks
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand citet
-key "KoTr02a,KoTr02b"
-
-\end_inset
-
- carefully benchmarked the spectral-element simulations of global seismic
- waves against normal-mode seismograms.
- Version 4.0 of
-\family typewriter
-SPECFEM3D_GLOBE
-\family default
- has been benchmarked again following the same procedure.
-
-\end_layout
-
-\begin_layout Standard
-In this appendix we present two tests: a `long-period' (periods longer than
- 17\InsetSpace ~
-s) simulation of a shallow event in isotropic PREM
-\begin_inset LatexCommand citep
-key "DzAn81"
-
-\end_inset
-
- without the ocean layer, without attenuation but including the effects
- of self-gravitation (in the Cowling approximation) (Figures
-\begin_inset LatexCommand ref
-reference "fig:Vanuatu-with-Vertical"
-
-\end_inset
-
- and
-\begin_inset LatexCommand ref
-reference "fig:Vanuatu-with-Transverse"
-
-\end_inset
-
-), and a `short-period' (periods longer than 9\InsetSpace ~
-s) simulation of a deep event
- in transversely isotropic PREM without the ocean layer and including the
- effects of self-gravitation and attenuation (Figures
-\begin_inset LatexCommand ref
-reference "fig:Bolivia-with-Vertical"
-
-\end_inset
-
-,
-\begin_inset LatexCommand ref
-reference "fig:Bolivia-with-Transverse"
-
-\end_inset
-
- and
-\begin_inset LatexCommand ref
-reference "fig:Bolivia-PKP"
-
-\end_inset
-
-).
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-placement h
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename /Users/sue/specfem3d/globe/USER_MANUAL/figures/vanuatu_vertical.eps
- scale 75
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Vanuatu-with-Vertical"
-
-\end_inset
-
- Normal-mode (blue) and SEM (red) vertical displacements in isotropic PREM
- considering the effects of self-gravitation but not attenuation for 13
- stations at increasing distance from the 1999 November 26th Vanuatu event
- located at 15\InsetSpace ~
-km depth.
- The SEM computation is accurate for periods longer than 17\InsetSpace ~
-s.
- The seismograms have been filtered between 50\InsetSpace ~
-s and 500\InsetSpace ~
-s.
- The station names are indicated on the left.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\begin_inset Float figure
-placement h
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename /Users/sue/specfem3d/globe/USER_MANUAL/figures/vanuatu_trans.eps
- scale 75
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Vanuatu-with-Transverse"
-
-\end_inset
-
-Same as in Figure
-\begin_inset LatexCommand ref
-reference "fig:Vanuatu-with-Vertical"
-
-\end_inset
-
- for the transverse displacements.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\begin_inset Float figure
-placement h
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename /Users/sue/specfem3d/globe/USER_MANUAL/figures/bolivia_vertical.eps
- scale 75
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Bolivia-with-Vertical"
-
-\end_inset
-
-Normal-mode (blue) and SEM (red) vertical displacements in transversely
- isotropic PREM considering the effects of self-gravitation and attenuation
- for 12 stations at increasing distance from the 1994 June 9th Bolivia event
- located at 647\InsetSpace ~
-km depth.
- The SEM computation is accurate for periods longer than 9\InsetSpace ~
-s.
- The seismograms have been filtered between 10\InsetSpace ~
-s and 500\InsetSpace ~
-s.
- The station names are indicated on the left.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\begin_inset Float figure
-placement h
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename /Users/sue/specfem3d/globe/USER_MANUAL/figures/bolivia_trans.eps
- scale 75
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Bolivia-with-Transverse"
-
-\end_inset
-
-Same as in Figure
-\begin_inset LatexCommand ref
-reference "fig:Bolivia-with-Vertical"
-
-\end_inset
-
- for the transverse displacements.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-placement h
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename /Users/sue/specfem3d/globe/USER_MANUAL/figures/PKPdf_all_15s500s.eps
- scale 75
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Bolivia-PKP"
-
-\end_inset
-
-Seismograms recorded between 130 degrees and 230 degrees, showing in particular
- the good agreement for core phases such as PKP.
- This figure is similar to Figure 24 of
-\begin_inset LatexCommand citet
-key "KoTr02a"
-
-\end_inset
-
-.
- The results have been filtered between 15\InsetSpace ~
-s and 500\InsetSpace ~
-s.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The normal-mode synthetics are calculated with the code
-\family typewriter
-QmXD
-\family default
- using mode catalogs with a shortest period of 8\InsetSpace ~
-s generated by the code
-
-\family typewriter
-OBANI
-\family default
-.
- No free-air, tilt, or gravitational potential corrections were applied
-
-\begin_inset LatexCommand citep
-key "DaTr98"
-
-\end_inset
-
-.
- We also turned off the effect of the oceans in
-\family typewriter
-QmXD
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-The normal-mode and SEM displacement seismograms are first calculated for
- a step source-time function, i.e., setting the parameter
-\family typewriter
-half
-\family default
-
-\family typewriter
-duration
-\family default
- in the
-\family typewriter
-CMTSOLUTION
-\family default
- file to zero for the SEM simulations.
- Both sets of seismograms are subsequently convolved with a triangular source-ti
-me function using the processing script
-\family typewriter
-UTILS/seis_
-\newline
-process/process_syn.pl
-\family default
-.
- They are also band-pass filtered and the horizontal components are rotated
- to the radial and transverse directions (with the script
-\family typewriter
-UTILS/seis_process/rotate.pl
-\family default
-).
-\end_layout
-
-\begin_layout Standard
-The match between the normal-mode and SEM seismograms is quite remarkable
- for the experiment with attenuation, considering the very different implementat
-ions of attenuation in the two computations (e.g., frequency domain versus
- time domain, constant Q versus absorption bands).
-\end_layout
-
-\begin_layout Standard
-Further tests can be found in the
-\family typewriter
-EXAMPLES
-\family default
- directory.
- It contains the normal-mode and SEM seismograms, and the parameters (
-\family typewriter
-STATIONS
-\family default
-,
-\family typewriter
-CMTSOLUTION
-\family default
- and
-\family typewriter
-Par_file
-\family default
-) for the SEM simulations.
-
-\end_layout
-
-\begin_layout Chapter
-\begin_inset LatexCommand label
-name "cha:License"
-
-\end_inset
-
-License
-\end_layout
-
-\begin_layout Standard
-
-\series bold
-GNU GENERAL PUBLIC LICENSE Version 2, June 1991.
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.
- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-\series default
-
-\newline
-
-\series medium
-Everyone is permitted to copy and distribute verbatim copies of this license
- document, but changing it is not allowed.
-\end_layout
-
-\begin_layout Section*
-Preamble
-\end_layout
-
-\begin_layout Standard
-The licenses for most software are designed to take away your freedom to
- share and change it.
- By contrast, the GNU General Public License is intended to guarantee your
- freedom to share and change free software -- to make sure the software
- is free for all its users.
- This General Public License applies to most of the Free Software Foundation's
- software and to any other program whose authors commit to using it.
- (Some other Free Software Foundation software is covered by the GNU Library
- General Public License instead.) You can apply it to your programs, too.
-\end_layout
-
-\begin_layout Standard
-When we speak of free software, we are referring to freedom, not price.
- Our General Public Licenses are designed to make sure that you have the
- freedom to distribute copies of free software (and charge for this service
- if you wish), that you receive source code or can get it if you want it,
- that you can change the software or use pieces of it in new free programs;
- and that you know you can do these things.
-\end_layout
-
-\begin_layout Standard
-To protect your rights, we need to make restrictions that forbid anyone
- to deny you these rights or to ask you to surrender the rights.
- These restrictions translate to certain responsibilities for you if you
- distribute copies of the software, or if you modify it.
-\end_layout
-
-\begin_layout Standard
-For example, if you distribute copies of such a program, whether gratis
- or for a fee, you must give the recipients all the rights that you have.
- You must make sure that they, too, receive or can get the source code.
- And you must show them these terms so they know their rights.
-\end_layout
-
-\begin_layout Standard
-We protect your rights with two steps:
-\end_layout
-
-\begin_layout Enumerate
-Copyright the software, and
-\end_layout
-
-\begin_layout Enumerate
-Offer you this license which gives you legal permission to copy, distribute
- and/or modify the software.
-\end_layout
-
-\begin_layout Standard
-Also, for each author's protection and ours, we want to make certain that
- everyone understands that there is no warranty for this free software.
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-\end_layout
-
-\begin_layout Standard
-Finally, any free program is threatened constantly by software patents.
- We wish to avoid the danger that redistributors of a free program will
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-\end_layout
-
-\begin_layout Standard
-The precise terms and conditions for copying, distribution and modification
- follow.
-\end_layout
-
-\begin_layout Section*
-GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION
- AND MODIFICATION
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
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-
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-\backslash
-begin{itemize}
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-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-item[0.]
-\end_layout
-
-\end_inset
-
-This License applies to any program or other work which contains a notice
- placed by the copyright holder saying it may be distributed under the terms
- of this General Public License.
- The ``Program'' below refers to any such program or work, and a ``work
- based on the Program'' means either the Program or any derivative work
- under copyright law: that is to say, a work containing the Program or a
- portion of it, either verbatim or with modifications and/or translated
- into another language.
- (Hereinafter, translation is included without limitation in the term ``modifica
-tion.'') Each licensee is addressed as ``you.''
-\newline
-
-\newline
-Activities other than copying,
- distribution and modification are not covered by this License; they are
- outside its scope.
- The act of running the Program is not restricted, and the output from the
- Program is covered only if its contents constitute a work based on the
- Program (independent of having been made by running the Program).
- Whether that is true depends on what the Program does.
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-end{itemize}
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Enumerate
-You may copy and distribute verbatim copies of the Program's source code
- as you receive it, in any medium, provided that you conspicuously and appropria
-tely publish on each copy an appropriate copyright notice and disclaimer
- of warranty; keep intact all the notices that refer to this License and
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-
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-
-\begin_deeper
-\begin_layout Standard
-You may charge a fee for the physical act of transferring a copy, and you
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-\end_deeper
-\begin_layout Enumerate
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- modifications or work under the terms of Section 1 above, provided that
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-\end_layout
-
-\begin_deeper
-\begin_layout Enumerate
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-\begin_layout Enumerate
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-
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-\begin_layout Enumerate
-If the modified program normally reads commands interactively when run,
- you must cause it, when started running for such interactive use in the
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- copyright notice and a notice that there is no warranty (or else, saying
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-\end_layout
-
-\begin_layout Standard
-These requirements apply to the modified work as a whole.
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- But when you distribute the same sections as part of a whole which is a
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-
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-
-\begin_layout Standard
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-\begin_layout Standard
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- the Program (or with a work based on the Program) on a volume of a storage
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-
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-
-\end_deeper
-\begin_layout Enumerate
-You may copy and distribute the Program (or a work based on it, under Section
- 2) in object code or executable form under the terms of Sections 1 and
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-\end_layout
-
-\begin_deeper
-\begin_layout Enumerate
-Accompany it with the complete corresponding machine-readable source code,
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-
-\begin_layout Enumerate
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-\end_layout
-
-\begin_layout Enumerate
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-\begin_layout Standard
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-\begin_layout Standard
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-\end_deeper
-\begin_layout Enumerate
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-\begin_layout Enumerate
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-\begin_layout Enumerate
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-\begin_layout Enumerate
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-\begin_deeper
-\begin_layout Standard
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-\begin_layout Standard
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-\begin_layout Standard
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-\end_deeper
-\begin_layout Enumerate
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-
-\end_layout
-
-\begin_layout Enumerate
-The Free Software Foundation may publish revised and/or new versions of
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Added: seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex (rev 0)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/USER_MANUAL/manual_SPECFEM3D_GLOBE.tex 2009-01-22 22:27:32 UTC (rev 13923)
@@ -0,0 +1,3284 @@
+%% LyX 1.5.1 created this file. For more info, see http://www.lyx.org/.
+%% Do not edit unless you really know what you are doing.
+\documentclass[oneside,english]{book}
+\usepackage[T1]{fontenc}
+\usepackage[latin1]{inputenc}
+\usepackage{geometry}
+\geometry{verbose,letterpaper,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
+\setcounter{secnumdepth}{3}
+\setcounter{tocdepth}{3}
+\usepackage{longtable}
+\usepackage{varioref}
+\usepackage{float}
+\usepackage{textcomp}
+\usepackage{amsmath}
+\usepackage{color}
+\usepackage{graphicx}
+\usepackage{amssymb}
+\IfFileExists{url.sty}{\usepackage{url}}
+ {\newcommand{\url}{\texttt}}
+\usepackage[authoryear]{natbib}
+
+\makeatletter
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
+%% Because html converters don't know tabularnewline
+\providecommand{\tabularnewline}{\\}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
+\newenvironment{lyxcode}
+{\begin{list}{}{
+\setlength{\rightmargin}{\leftmargin}
+\setlength{\listparindent}{0pt}% needed for AMS classes
+\raggedright
+\setlength{\itemsep}{0pt}
+\setlength{\parsep}{0pt}
+\normalfont\ttfamily}%
+ \item[]}
+{\end{list}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
+% fonts
+\usepackage{times}
+\usepackage{natbib}
+
+% date of last edit
+\date{\today}
+
+% create thumbnails
+\usepackage[pdftex]{thumbpdf}
+
+% hyperlinks to sections and references
+\usepackage[pdftex,bookmarks=true,bookmarksnumbered=true,pdfpagemode=None,pdfstartview=FitH,pdfpagelayout=SinglePage,pdfborder={0 0 0}]{hyperref}
+
+\let\myUrl\url
+\renewcommand{\url}[1]{(\myUrl{#1})}
+
+% biblio GJI
+\bibliographystyle{abbrvnat}
+
+\newcommand{\toall}[1]{\textbf{*** All: #1 ***}}
+\newcommand{\tojeroen}[1]{\textbf{*** Jeroen: #1 ***}}
+\newcommand{\tobrian}[1]{\textbf{*** Brian: #1 ***}}
+\newcommand{\tovala}[1]{\textbf{*** Vala: #1 ***}}
+\newcommand{\tovalabrian}[1]{\textbf{*** Vala \& Brian: #1 ***}}
+\newcommand{\tovalaqinya}[1]{\textbf{*** Vala \& Qinya: #1 ***}}
+\newcommand{\toqinya}[1]{\textbf{*** Qinya: #1 ***}}
+\newcommand{\tomin}[1]{\textbf{*** Min: #1 ***}}
+\newcommand{\toalessia}[1]{\textbf{*** Alessia: #1 ***}}
+\newcommand{\todimitri}[1]{\textbf{*** Dimitri: #1 ***}}
+
+\newcommand{\nexxi}{\mbox{\texttt{NEX\_XI}}}
+\newcommand{\nexeta}{\mbox{\texttt{NEX\_ETA}}}
+\newcommand{\nprocxi}{\mbox{\texttt{NPROC\_XI}}}
+\newcommand{\nproceta}{\mbox{\texttt{NPROC\_ETA}}}
+\newcommand{\nchunks}{\mbox{\texttt{NCHUNKS}}}
+
+\usepackage{babel}
+\makeatother
+
+\begin{document}
+\begin{center}
+\thispagestyle{empty}\textbf{}%
+\begin{figure}[H]
+\noindent \includegraphics[width=0.75\paperwidth]{figures/specfem_3d_globe-cover}
+\end{figure}
+
+\par\end{center}
+
+
+\title{\thispagestyle{empty}\textbf{SPECFEM3D\_GLOBE}\\
+\textbf{User Manual}}
+
+
+\author{© California Institute of Technology (U.S.) and\\
+University of Pau / CNRS / INRIA (France)\\
+Version 4.0}
+
+
+\date{\noindent \today}
+
+\maketitle
+\tableofcontents{}
+
+
+\chapter{Introduction}
+
+\textit{{}``Petaflops for your seismograms''}
+
+The software package SPECFEM3D\_GLOBE simulates three-dimensional
+global and regional seismic wave propagation based upon the spectral-element
+method (SEM). Effects due to lateral variations in compressional-wave
+speed, shear-wave speed, density, a 3D crustal model, ellipticity,
+topography and bathymetry, the oceans, rotation, and self-gravitation
+are included. For a detailed introduction to the SEM as applied to
+global and regional seismic wave propagation, please consult \citet{KoVi98,KoTr99,Ch00,KoTr02a,KoTr02b,KoRiTr02,ChCaVi03,CaChViMo03,ChVa04}.
+If you use 3D mantle model S20RTS, please cite \citet{RiVaWo99}.
+The package can accommodate full 21-parameter anisotropy \citep{ChTr07}
+as well as lateral variations in attenuation \citep{SavWiTr05}. Adjoint
+capabilities and finite-frequency kernel simulations are also included
+\citep{LiTr06,LiTr08}.
+
+All SPECFEM3D\_GLOBE software is written in Fortran90 with full portability
+in mind, and conforms strictly to the Fortran95 standard. It uses
+no obsolete or obsolescent features of Fortran77. The package uses
+parallel programming based upon the Message Passing Interface (MPI)
+\citep{GrLuSk94,Pac97}.
+
+SPECFEM3D won the Gordon Bell award for best performance at the SuperComputing~2003
+conference in Phoenix, Arizona (U.S.) by running at 5 teraflops (sustained)
+on 1944 processors of the Japanese Earth Simulator using 14.6 billion
+degrees of freedom stored in 2.5 terabytes of memory; see \cite{KoTsChTr03}
+and the Gordon Bell Awards News Release \url{www.sc-conference.org/sc2003/nr_finalaward.html }
+for details.
+
+
+\section{Citation}
+
+If you use SPECFEM3D\_GLOBE for your own research, please cite at
+least one of the following articles: \cite {KoRiTr02,KoTr02a,KoTr02b,KoTr99}
+or \cite{KoVi98}. The corresponding Bib\TeX{} entries may be found
+in file \texttt{USER\_MANUAL/bibliography.bib} or in comments at the
+beginning of file \texttt{specfem3D.f90}.
+
+
+\section{Support}
+
+This material is based upon work supported by the U.S. National Science
+Foundation under Grants No. EAR-0406751 and EAR-0711177, by the French
+CNRS, French INRIA Sud-Ouest MAGIQUE-3D, French ANR NUMASIS under
+Grant No. ANR-05-CIGC-002, and European FP6 Marie Curie International
+Reintegration Grant No. MIRG-CT-2005-017461. Any opinions, findings,
+and conclusions or recommendations expressed in this material are
+those of the authors and do not necessarily reflect the views of the
+U.S. National Science Foundation, CNRS, INRIA, ANR or the European
+Marie Curie program.
+
+
+\chapter{\label{cha:Getting-Started}Getting Started}
+
+The SPECFEM3D\_GLOBE software package comes in a gzipped tar ball.
+In the directory in which you want to install the package, type
+
+\begin{lyxcode}
+tar~-zxvf~SPECFEM3D\_GLOBE\_V4.0.0.tar.gz
+\end{lyxcode}
+The directory \texttt{SPECFEM3D\_GLOBE\_V4.0.0} will then contain
+the source code.
+
+To configure the software for your system, run the \texttt{configure}
+shell script. This script will attempt to guess the appropriate configuration
+values for your system. However, at a minimum, it is recommended that
+you explicitly specify the appropriate command names for your Fortran90
+compiler and MPI package:
+
+\begin{lyxcode}
+./configure~FC=ifort~MPIFC=mpif90
+\end{lyxcode}
+A summary of the most important configuration variables follows.
+
+\begin{description}
+\item [{\texttt{FC}}] Fortran90 compiler command name. By default, \texttt{configure}
+will execute the command names of various well-known Fortran compilers
+in succession, picking the first one it finds that works.
+\item [{\texttt{MPIFC}}] MPI Fortran90 command name. The default is \texttt{mpif90}.
+This must correspond to the same underlying compiler specified by
+\texttt{FC}; otherwise, you will encounter compilation or link errors
+when you attempt to build the code. If you are unsure about this,
+it is usually safe to set both \texttt{FC} and \texttt{MPIFC} to the
+MPI compiler command for your system:
+\end{description}
+\begin{lyxcode}
+./configure~FC=mpif90~MPIFC=mpif90
+\end{lyxcode}
+\begin{description}
+\item [{\texttt{FLAGS\_CHECK}}] Compiler flags for non-critical subroutines.
+\item [{\texttt{FLAGS\_NO\_CHECK}}] Compiler flags for creating fast, production-run
+code for critical subroutines.
+\item [{\texttt{LOCAL\_PATH\_IS\_ALSO\_GLOBAL}}] Set to \texttt{.false.}
+on most cluster applications. For reasons of speed, the (parallel)
+mesher typically writes a (parallel) database for the solver on the
+local disks of the compute nodes. Some systems have no local disks
+(e.g., BlueGene or the Earth Simulator) and other systems have a fast
+parallel file system, in which case this variable should be set to
+\texttt{.true.}. Note that this flag is not used by the mesher or
+the solver; it is only used for some of the post-processing.
+\end{description}
+In addition to reading configuration variables, \texttt{configure}
+accepts the following options:
+
+\begin{description}
+\item [{\texttt{-{}-enable-double-precision}}] The package can run either
+in single or in double precision. The default is single precision
+mode because this requires exactly half as much memory. To specify
+double precision mode, simply provide \texttt{-{}-enable-double-precision}
+as a command-line argument to \texttt{configure}. On a new system,
+it is definitely worth experimenting with single versus double precision
+simulations to determine which is faster. Note that on many current
+processors (e.g., Intel, AMD, IBM Power), single precision calculations
+are often significantly faster; the difference can typically be 10\%
+to 25\%. It is therefore worth trying single precision if you can.
+We recommend running the same calculation once in single precision
+and in double precision on your system and comparing the seismograms.
+If they are identical, you should probably select single precision
+for your future runs.
+\item [{\texttt{-{}-help}}] Directs \texttt{configure} to print a usage
+screen which provides a short description of all configuration variables
+and options. Note that the options relating to installation directories
+(e.g., \texttt{-{}-prefix}) do not apply to SPECFEM3D\_GLOBE.
+\end{description}
+The \texttt{configure} script runs a brief series of checks. Upon
+successful completion, it generates the files \texttt{Makefile}, \texttt{constants.h},
+and \texttt{precision.h} in the working directory.
+
+\begin{description}
+\item [{Note:}] If the \texttt{configure} script fails, and you don't know
+what went wrong, examine the log file \texttt{config.log}. This file
+contains a detailed transcript of all the checks \texttt{configure}
+performed. Most importantly, it includes the error output (if any)
+from your compiler.
+\end{description}
+The \texttt{configure} script automatically runs the script \texttt{flags.guess}.
+This helper script contains a number of suggested flags for various
+compilers; e.g., Portland, Intel, Absoft, NAG, Lahey, NEC, IBM and
+SGI. The software has run on a wide variety of compute platforms,
+e.g., various PC clusters and machines from Sun, SGI, IBM, Compaq,
+and NEC. The \texttt{flags.guess} script attempts to guess which compiler
+you are using (based upon the compiler command name) and choose the
+related optimization flags. The \texttt{configure} script then automatically
+inserts the suggested flags into \texttt{Makefile}. Note that \texttt{flags.guess}
+may fail to identify your compiler; and in any event, the default
+flags chosen by \texttt{flags.guess} are undoubtedly not optimal for
+your system. So, we encourage you to experiment with these flags (by
+editing the generated \texttt{Makefile} by hand) and to solicit advice
+from your system administrator. Selecting the right compiler and compiler
+flags can make a tremendous difference in terms of performance. We
+welcome feedback on your experience with various compilers and flags.
+
+On SGI systems, \texttt{flags.guess} automatically informs \texttt{configure}
+to insert `\texttt{`TRAP\_FPE=OFF}'' into the generated \texttt{Makefile}
+in order to turn underflow trapping off.
+
+Finally, before compiling, make sure that the subdirectories \texttt{obj},
+\texttt{bak} and \texttt{OUTPUT\_FILES} exist within the directory
+with the source code (\texttt{SPECFEM3D\_GLOBE\_V4.0.0}). The \texttt{go\_mesher}
+script discussed below automatically takes care of creating the \texttt{OUTPUT\_FILES}
+directory.
+
+Note that if you run very large meshes on a relatively small number
+of processors, the memory size needed on each processor might become
+greater than 2 gigabytes, which is the upper limit for 32-bit addressing;
+in this case, on some compilers you may need to add \texttt{``-mcmodel=medium}''
+to the compiler options otherwise the compiler will display an error
+message.
+
+
+\chapter{\label{cha:Running-the-Mesher}Running the Mesher \texttt{xmeshfem3D}}
+
+You are now ready to compile the mesher. In the directory with the
+source code, 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}.
+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,Ch00,KoTr02a,KoTr02b,KoRiTr02,ChCaVi03,CaChViMo03}
+and \citet{ChVa04}. A detailed theoretical analysis of the dispersion
+and stability properties of the SEM is available in \citet{DeSe07}
+and \citet{SeOl07}.
+
+In this chapter we will focus on simulations at the scale of the entire
+globe. Regional simulations will be addressed in Chapter~\ref{cha:Regional-Simulations}.
+The spectral-element mesh for a SPECFEM3D\_GLOBE simulation is based
+upon a mapping from the cube to the sphere called the \textit{cubed
+sphere} \citep{Sad72,RoIaPa96}. This cubed-sphere mapping breaks
+the globe into 6~chunks, each of which is further subdivided in terms
+of $n^{2}$ mesh slices, where $n\ge1$ is a positive integer, for
+a total of $6\times n^{2}$ slices (Figure~\ref{figure:mpi_slices}).
+Thus the minimum number of processors required for a global simulation
+is 6 (although it is theoretically possible to run more than one slice
+per processor). %
+\begin{figure}
+\centerline{ \begin{tabular}{cc}
+\includegraphics[width=0.45\textwidth]{figures/mpi_slices} & \includegraphics[width=0.45\textwidth]{figures/fullmesh_18} \tabularnewline
+\end{tabular}}
+
+\caption{Each of the 6~chunks that constitutes the cubed sphere is subdivided
+in terms of $n^{2}$~slices of elements, where $n\ge1$ is a positive
+integer, for a total of $6\times n^{2}$ slices (and therefore processors).
+The figure on the left shows a mesh that is divided in terms of $6\times5^{2}=150$
+slices as indicated by the various colors. In this cartoon, each slice
+contains $5\times5=25$ spectral elements at the Earth's surface.
+The figure on the right shows a mesh that is divided over $6\times18^{2}=1944$
+processors as indicated by the various colors. Regional simulations
+can be accommodated by using only 1, 2 or 3 chunks of the cubed sphere.
+One-chunk simulations may involve a mesh with lateral dimensions smaller
+than~$90^{\circ}$, thereby accommodating smaller-scale simulations. }
+
+
+\label{figure:mpi_slices}
+\end{figure}
+
+
+To run the mesher for a global simulation, the following parameters
+need to be set in 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{NCHUNKS}}] must be set to 6 for global simulations.
+\item [{\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}}] Not needed for a global
+simulation. (See Chapter~\ref{cha:Regional-Simulations} for regional
+simulations.)
+\item [{\texttt{ANGULAR\_WIDTH\_ETA\_IN\_DEGREES}}] Not needed for a global
+simulation. (See Chapter~\ref{cha:Regional-Simulations} for regional
+simulations.)
+\item [{\texttt{CENTER\_LATITUDE\_IN\_DEGREES}}] Not needed for a global
+simulation. (See Chapter~\ref{cha:Regional-Simulations} for regional
+simulations.)
+\item [{\texttt{CENTER\_LONGITUDE\_IN\_DEGREES}}] Not needed for a global
+simulation. (See Chapter~\ref{cha:Regional-Simulations} for regional
+simulations.)
+\item [{\texttt{GAMMA\_ROTATION\_AZIMUTH}}] Not needed for a global simulation.
+(See Chapter~\ref{cha:Regional-Simulations} for regional simulations.)
+\item [{$\nexxi$}] The number of spectral elements along one side of a
+chunk in the cubed sphere (see Figure~\ref{figure:mpi_slices});
+this number \textit{must} be a multiple of 16 and 8~$\times$~a
+multiple of $\nprocxi$ defined below. We do not recommend using $\nexxi$
+less than 64 because the curvature of the Earth cannot be honored
+if one uses too few elements, and distorted elements can lead to inaccurate
+and unstable simulations, i.e., smaller values of $\nexxi$ are likely
+to result in spectral elements with a negative Jacobian, in which
+case the mesher will exit with an error message. Table~\ref{table:nex}
+summarizes various suitable choices for $\nexxi$ and the related
+values of $\nprocxi$. Based upon benchmarks against semi-analytical
+normal-mode synthetic seismograms, \citet{KoTr02a,KoTr02b} determined
+that a $\nexxi=256$ run is accurate to a shortest period of roughly
+17~s. Therefore, since accuracy is determined by the number of grid
+points per shortest wavelength, for any particular value of $\nexxi$
+the simulation will be accurate to a shortest period determined approximately
+by \begin{equation}
+\mbox{shortest period (s)}\simeq(256/\nexxi)\times17.\label{eq:shortest_period}\end{equation}
+ The number of grid points in each orthogonal direction of the reference
+element, i.e., the number of Gauss-Lobatto-Legendre points, is determined
+by \texttt{NGLLX} in the \texttt{constants.h} file. In the globe we
+use $\mbox{\texttt{NGLLX}}=5$, for a total of $5^{3}=125$ points
+per elements. We suggest not to change this value.
+\item [{$\nexeta$}] For global simulations $\nexeta$ must be set to the
+same value as $\nexxi$.
+\item [{$\nprocxi$}] The number of processors or slices along one chunk
+of the cubed sphere (see Figure~\ref{figure:mpi_slices}); we must
+have $\nexxi=8\times c\times\nprocxi$, where $c\ge1$ is a positive
+integer. See Table~\ref{table:nex} for various suitable choices.
+\item [{$\nproceta$}] For global simulations $\nproceta$ must be set
+to the same value as $\nprocxi$.
+\item [{\texttt{MODEL}}] Must be set to one of the following:
+\item [{\textmd{1D~models~with~real~structure:}}]~
+
+\begin{description}
+\item [{\texttt{1D\_isotropic\_prem}}] Isotropic version of the spherically
+symmetric Preliminary Reference Earth Model (PREM) \citep{DzAn81}.
+\item [{\texttt{1D\_transversely\_isotropic\_prem}}] Transversely isotropic
+version of PREM.
+\item [{\texttt{1D\_iasp91}}] Spherically symmetric isotropic IASP91 model
+\citep{KeEn91}.
+\item [{\texttt{1D\_1066a}}] Spherically symmetric earth model 1066A \citep{gilbertdziewonski1975}.
+When \texttt{\small ATTENTUATION} is on, it uses an unpublished 1D
+attenuation model from Scripps.
+\item [{\texttt{1D\_ak135}}] Spherically symmetric isotropic AK135 model
+\citep{KeEnBu95}.
+\item [{\texttt{1}D\_ref}] A recent 1D Earth model developed by \citet{KuDzEk06}.
+This model is the 1D background model for the 3D models s362ani, s362wmani,
+s362ani\_prem, and s29ea.
+\end{description}
+\end{description}
+For historical reasons and to provide benchmarks against normal-mode
+synthetics, the mesher accommodates versions of various 1D models
+with a single crustal layer with the properties of the original upper
+crust. These `one-crust' models are:
+
+\texttt{1D\_isotropic\_prem\_onecrust}
+
+\texttt{1D\_transversely\_isotropic\_prem\_onecrust}
+
+\texttt{1D\_iasp91\_onecrust}, \texttt{1D\_1066a\_onecrust}
+
+\texttt{1D\_ak135\_onecrust}
+
+\begin{description}
+\item [{\textmd{Fully~3D~models:}}]~
+
+\begin{description}
+\item [{\texttt{transversely\_isotropic\_prem\_plus\_3D\_crust\_2.0}}] This
+model has CRUST2.0 \citep{BaLaMa00} on top of a transversely isotropic
+PREM. We first extrapolate PREM mantle velocity up to the surface,
+then overwrite the model with CRUST2.0
+\item [{\texttt{s20rts}}] By default, the code uses 3D mantle model S20RTS
+\citep{RiVaWo99} and 3D crustal model Crust2.0 \citep{BaLaMa00}.
+Note that S20RTS uses transversely isotropic PREM as a background
+model, and that we use the PREM radial attenuation model when \texttt{ATTENUATION}
+is incorporated. See Chapter~\ref{cha:-Changing-the} for a discussion
+on how to change 3D models.
+\item [{\texttt{\textcolor{black}{s362ani}}}] A global shear-wave speed
+model developed by \citet{KuDzEk06}. In this model, radial anisotropy
+is confined to the uppermost mantle. The model (and the corresponding
+mesh) incorporate tomography on the 650\textasciitilde{}km and 410\textasciitilde{}km
+discontinuities in the 1D reference model REF.
+\item [{\texttt{\textcolor{black}{s362wmani}}}] A version of S362ANI with
+anisotropy allowed throughout the mantle.
+\item [{\texttt{\textcolor{black}{s362ani\_prem}}}] A version of S362ANI
+calculated using PREM as the 1D reference model.
+\item [{\texttt{\textcolor{black}{s29ea}}}] A global model with higher
+resolution in the upper mantle beneath Eurasia calculated using REF
+as the 1D reference model.
+\item [{\texttt{3D\_anisotropic}}] See Chapter~\ref{cha:-Changing-the}
+for a discussion on how to specify your own 3D anisotropic model.
+\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 [{\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{ELLIPTICITY}}] Set to \texttt{.true.} if the mesh should
+make the Earth model elliptical in shape according to Clairaut's equation
+\citep{DaTr98}. This feature adds no cost to the simulation.
+\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{GRAVITY}}] Set to \texttt{.true.} if self-gravitation should
+be incorporated in the Cowling approximation \citep{KoTr02b,DaTr98}.
+Turning this feature on is relatively inexpensive, both from the perspective
+of memory requirements as well as in terms of computational speed.
+\item [{\texttt{ROTATION}}] Set to \texttt{.true.} if the Coriolis effect
+should be incorporated. Turning this feature on is relatively cheap
+numerically.
+\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. Of course for realistic simulations this flag should be
+turned on. See \citet{KoTr99,KoTr02a} for a discussion on the implementation
+of attenuation based upon standard linear solids.
+\item [{\texttt{ABSORBING\_CONDITIONS}}] Set to \texttt{.false.} for global
+simulations. See Chapter~\ref{cha:Regional-Simulations} for regional
+simulations.
+\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{HDUR\_MOVIE}}] determines the half duration of the source
+time function for the movie simulations. When this parameter is set
+to be 0, a default half duration that corresponds to the accuracy
+of the simulation is provided.
+\item [{\texttt{SAVE\_MESH\_FILES}}] Set this flag to \texttt{.true}\texttt{\small .}
+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:Meshes}
+for a discussion of mesh viewing features.
+\item [{\texttt{NUMBER\_OF\_RUNS}}] On machines with a run-time limit,
+for instance for a batch/queue system, a simulation may need to be
+completed in stages. This option allows you to select the number of
+stages in which the simulation will be completed (1, 2 or 3). Choose
+1 for a run without restart files. This feature is not used at the
+time of meshing but is required for the solver. At the end of the
+first or second stage of a multi-stage simulation, large files are
+written to the file system to save the current state of the simulation.
+This state is read back from the file system at the beginning of the
+next stage of the multi-stage run. Reading and writing the states
+can be very time consuming depending on the nature of the network
+and the file system (in this case writing to the local file system,
+i.e., the disk on a node, is preferable).
+\item [{\texttt{NUMBER\_OF\_THIS\_RUN}}] If you choose to perform the run
+in stages, you need to tell the solver what stage run to perform.
+This feature is not used at the time of meshing but is required for
+the solver.
+\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
+are written on a parallel (global) file system (see also the earlier
+discussion of the \texttt{LOCAL\_PATH\_IS\_ALSO\_GLOBAL} flag in Chapter~\ref{cha:Getting-Started}).
+The mesher generates the necessary databases in parallel, one set
+for each of the $6\times\nprocxi^{2}$ slices that constitutes the
+mesh (see Figure~\ref{figure:mpi_slices}). After the 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. The seismograms can be created in three different formats
+by setting the parameters \texttt{OUTPUT\_SEISMOS\_ASCII\_TEXT}, \texttt{OUTPUT\_SEISMOS\_SAC\_ALPHANUM}
+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
+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
+to avoid writing to the seismograms too often. This feature is not
+used at the time of meshing.
+\item [{\texttt{NTSTEP\_BETWEEN\_READ\_ADJSRC}}] The number of adjoint
+sources read in each time for an adjoint simulation.
+\item [{\texttt{OUTPUT\_SEISMOS\_ASCII\_TEXT}}] Set this flag to \texttt{.true.}
+if you want to have the synthetic seismograms written in two-column
+ASCII format (the first column contains time in seconds and the second
+column the displacement in meters of the recorded signal, no header
+information). Files will be named with extension \texttt{.ascii}.
+\item [{\texttt{OUTPUT\_SEISMOS\_SAC\_ALPHANUM}}] Set this flag to \texttt{.true.}
+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}.
+\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}.
+\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.} $\rightarrow$
+East (E) and North (N) components).
+\item [{\texttt{WRITE\_SEISMOGRAMS\_BY\_MASTER}}] Set this flag to \texttt{.true.}
+if you want to have all the seismograms written by the master (no
+need to collect them on the nodes after the run).
+\item [{\texttt{SAVE\_ALL\_SEISMOS\_IN\_ONE\_FILE}}] Set this flag to \texttt{.true.}
+if you want to have all the seismograms saved in one large combined
+file instead of one file per seismogram to avoid overloading shared
+non-local file systems such as GPFS for instance.
+\item [{\texttt{USE\_BINARY\_FOR\_LARGE\_FILE}}] Set this flag to \texttt{.true.}
+if you want to use binary instead of ASCII for that large file (not
+used if SAVE\_ALL\_SEISMOS\_IN \_ONE\_FILE = .false.)
+\item [{\texttt{RECEIVERS\_CAN\_BE\_BURIED}}] This flag accommodates stations
+with instruments that are buried, i.e., the solver will calculate
+seismograms at the burial depth specified in the \texttt{STATIONS}
+file. 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}
+\noindent \begin{center}
+\label{table:nex} \begin{longtable}{|c|c|c|c|c|c|c|c|c|c|c|c|}
+\hline
+\nprocxi & processors & \multicolumn{10}{c|}{\nexxi}\tabularnewline
+\hline
+\endhead
+\hline
+1 & 6 & 64 & 80 & 96 & 112 & 128 & 144 & 160 & 176 & 192 & 208\tabularnewline
+\hline
+2 & 24 & 64 & 80 & 96 & 112 & 128 & 144 & 160 & 176 & 192 & 208\tabularnewline
+\hline
+3 & 54 & 96 & 144 & 192 & 240 & 288 & 336 & 384 & 432 & 480 & 528\tabularnewline
+\hline
+4 & 96 & 64 & 96 & 128 & 160 & 192 & 224 & 256 & 288 & 320 & 352\tabularnewline
+\hline
+5 & 150 & 80 & 160 & 240 & 320 & 400 & 480 & 560 & 640 & 720 & 800\tabularnewline
+\hline
+6 & 216 & 96 & 144 & 192 & 240 & 288 & 336 & 384 & 432 & 480 & 528\tabularnewline
+\hline
+7 & 294 & 112 & 224 & 336 & 448 & 560 & 672 & 784 & 896 & 1008 & 1120\tabularnewline
+\hline
+8 & 384 & 64 & 128 & 192 & 256 & 320 & 384 & 448 & 512 & 576 & 640\tabularnewline
+\hline
+9 & 486 & 144 & 288 & 432 & 576 & 720 & 864 & 1008 & 1152 & 1296 & 1440\tabularnewline
+\hline
+10 & 600 & 80 & 160 & 240 & 320 & 400 & 480 & 560 & 640 & 720 & 800\tabularnewline
+\hline
+11 & 726 & 176 & 352 & 528 & 704 & 880 & 1056 & 1232 & 1408 & 1584 & 1760\tabularnewline
+\hline
+12 & 864 & 96 & 192 & 288 & 384 & 480 & 576 & 672 & 768 & 864 & 960\tabularnewline
+\hline
+13 & 1014 & 208 & 416 & 624 & 832 & 1040 & 1248 & 1456 & 1664 & 1872 & 2080\tabularnewline
+\hline
+14 & 1176 & 112 & 224 & 336 & 448 & 560 & 672 & 784 & 896 & 1008 & 1120\tabularnewline
+\hline
+15 & 1350 & 240 & 480 & 720 & 960 & 1200 & 1440 & 1680 & 1920 & 2160 & 2400\tabularnewline
+\hline
+16 & 1536 & 128 & 256 & 384 & 512 & 640 & 768 & 896 & 1024 & 1152 & 1280\tabularnewline
+\hline
+17 & 1734 & 272 & 544 & 816 & 1088 & 1360 & 1632 & 1904 & 2176 & 2448 & 2720\tabularnewline
+\hline
+18 & 1944 & 144 & 288 & 432 & 576 & 720 & 864 & 1008 & 1152 & 1296 & 1440\tabularnewline
+\hline
+19 & 2166 & 304 & 608 & 912 & 1216 & 1520 & 1824 & 2128 & 2432 & 2736 & 3040\tabularnewline
+\hline
+20 & 2400 & 160 & 320 & 480 & 640 & 800 & 960 & 1120 & 1280 & 1440 & 1600\tabularnewline
+\hline
+21 & 2646 & 336 & 672 & 1008 & 1344 & 1680 & 2016 & 2352 & 2688 & 3024 & 3360\tabularnewline
+\hline
+22 & 2904 & 176 & 352 & 528 & 704 & 880 & 1056 & 1232 & 1408 & 1584 & 1760\tabularnewline
+\hline
+23 & 3174 & 368 & 736 & 1104 & 1472 & 1840 & 2208 & 2576 & 2944 & 3312 & 3680\tabularnewline
+\hline
+24 & 3456 & 192 & 384 & 576 & 768 & 960 & 1152 & 1344 & 1536 & 1728 & 1920\tabularnewline
+\hline
+25 & 3750 & 400 & 800 & 1200 & 1600 & 2000 & 2400 & 2800 & 3200 & 3600 & 4000\tabularnewline
+\hline
+26 & 4056 & 208 & 416 & 624 & 832 & 1040 & 1248 & 1456 & 1664 & 1872 & 2080\tabularnewline
+\hline
+27 & 4374 & 432 & 864 & 1296 & 1728 & 2160 & 2592 & 3024 & 3456 & 3888 & 4320\tabularnewline
+\hline
+28 & 4704 & 224 & 448 & 672 & 896 & 1120 & 1344 & 1568 & 1792 & 2016 & 2240\tabularnewline
+\hline
+29 & 5046 & 464 & 928 & 1392 & 1856 & 2320 & 2784 & 3248 & 3712 & 4176 & 4640\tabularnewline
+\hline
+30 & 5400 & 240 & 480 & 720 & 960 & 1200 & 1440 & 1680 & 1920 & 2160 & 2400\tabularnewline
+\hline
+31 & 5766 & 496 & 992 & 1488 & 1984 & 2480 & 2976 & 3472 & 3968 & 4464 & 4960\tabularnewline
+\hline
+32 & 6144 & 256 & 512 & 768 & 1024 & 1280 & 1536 & 1792 & 2048 & 2304 & 2560\tabularnewline
+\hline
+33 & 6534 & 528 & 1056 & 1584 & 2112 & 2640 & 3168 & 3696 & 4224 & 4752 & 5280\tabularnewline
+\hline
+34 & 6936 & 272 & 544 & 816 & 1088 & 1360 & 1632 & 1904 & 2176 & 2448 & 2720\tabularnewline
+\hline
+35 & 7350 & 560 & 1120 & 1680 & 2240 & 2800 & 3360 & 3920 & 4480 & 5040 & 5600\tabularnewline
+\hline
+36 & 7776 & 288 & 576 & 864 & 1152 & 1440 & 1728 & 2016 & 2304 & 2592 & 2880\tabularnewline
+\hline
+37 & 8214 & 592 & 1184 & 1776 & 2368 & 2960 & 3552 & 4144 & 4736 & 5328 & 5920\tabularnewline
+\hline
+38 & 8664 & 304 & 608 & 912 & 1216 & 1520 & 1824 & 2128 & 2432 & 2736 & 3040\tabularnewline
+\hline
+39 & 9126 & 624 & 1248 & 1872 & 2496 & 3120 & 3744 & 4368 & 4992 & 5616 & 6240\tabularnewline
+\hline
+40 & 9600 & 320 & 640 & 960 & 1280 & 1600 & 1920 & 2240 & 2560 & 2880 & 3200\tabularnewline
+\hline
+41 & 10086 & 656 & 1312 & 1968 & 2624 & 3280 & 3936 & 4592 & 5248 & 5904 & 6560\tabularnewline
+\hline
+42 & 10584 & 336 & 672 & 1008 & 1344 & 1680 & 2016 & 2352 & 2688 & 3024 & 3360\tabularnewline
+\hline
+43 & 11094 & 688 & 1376 & 2064 & 2752 & 3440 & 4128 & 4816 & 5504 & 6192 & 6880\tabularnewline
+\hline
+44 & 11616 & 352 & 704 & 1056 & 1408 & 1760 & 2112 & 2464 & 2816 & 3168 & 3520\tabularnewline
+\hline
+45 & 12150 & 720 & 1440 & 2160 & 2880 & 3600 & 4320 & 5040 & 5760 & 6480 & 7200\tabularnewline
+\hline
+46 & 12696 & 368 & 736 & 1104 & 1472 & 1840 & 2208 & 2576 & 2944 & 3312 & 3680\tabularnewline
+\hline
+47 & 13254 & 752 & 1504 & 2256 & 3008 & 3760 & 4512 & 5264 & 6016 & 6768 & 7520\tabularnewline
+\hline
+48 & 13824 & 384 & 768 & 1152 & 1536 & 1920 & 2304 & 2688 & 3072 & 3456 & 3840\tabularnewline
+\hline
+49 & 14406 & 784 & 1568 & 2352 & 3136 & 3920 & 4704 & 5488 & 6272 & 7056 & 7840\tabularnewline
+\hline
+50 & 15000 & 400 & 800 & 1200 & 1600 & 2000 & 2400 & 2800 & 3200 & 3600 & 4000\tabularnewline
+\hline
+51 & 15606 & 816 & 1632 & 2448 & 3264 & 4080 & 4896 & 5712 & 6528 & 7344 & 8160\tabularnewline
+\hline
+52 & 16224 & 416 & 832 & 1248 & 1664 & 2080 & 2496 & 2912 & 3328 & 3744 & 4160\tabularnewline
+\hline
+53 & 16854 & 848 & 1696 & 2544 & 3392 & 4240 & 5088 & 5936 & 6784 & 7632 & 8480\tabularnewline
+\hline
+54 & 17496 & 432 & 864 & 1296 & 1728 & 2160 & 2592 & 3024 & 3456 & 3888 & 4320\tabularnewline
+\hline
+55 & 18150 & 880 & 1760 & 2640 & 3520 & 4400 & 5280 & 6160 & 7040 & 7920 & 8800\tabularnewline
+\hline
+56 & 18816 & 448 & 896 & 1344 & 1792 & 2240 & 2688 & 3136 & 3584 & 4032 & 4480\tabularnewline
+\hline
+57 & 19494 & 912 & 1824 & 2736 & 3648 & 4560 & 5472 & 6384 & 7296 & 8208 & 9120\tabularnewline
+\hline
+58 & 20184 & 464 & 928 & 1392 & 1856 & 2320 & 2784 & 3248 & 3712 & 4176 & 4640\tabularnewline
+\hline
+59 & 20886 & 944 & 1888 & 2832 & 3776 & 4720 & 5664 & 6608 & 7552 & 8496 & 9440\tabularnewline
+\hline
+60 & 21600 & 480 & 960 & 1440 & 1920 & 2400 & 2880 & 3360 & 3840 & 4320 & 4800\tabularnewline
+\hline
+61 & 22326 & 976 & 1952 & 2928 & 3904 & 4880 & 5856 & 6832 & 7808 & 8784 & 9760\tabularnewline
+\hline
+62 & 23064 & 496 & 992 & 1488 & 1984 & 2480 & 2976 & 3472 & 3968 & 4464 & 4960\tabularnewline
+\hline
+63 & 23814 & 1008 & 2016 & 3024 & 4032 & 5040 & 6048 & 7056 & 8064 & 9072 & 10080\tabularnewline
+\hline
+64 & 24576 & 512 & 1024 & 1536 & 2048 & 2560 & 3072 & 3584 & 4096 & 4608 & 5120\tabularnewline
+\hline
+65 & 25350 & 1040 & 2080 & 3120 & 4160 & 5200 & 6240 & 7280 & 8320 & 9360 & 10400\tabularnewline
+\hline
+66 & 26136 & 528 & 1056 & 1584 & 2112 & 2640 & 3168 & 3696 & 4224 & 4752 & 5280\tabularnewline
+\hline
+67 & 26934 & 1072 & 2144 & 3216 & 4288 & 5360 & 6432 & 7504 & 8576 & 9648 & 10720\tabularnewline
+\hline
+68 & 27744 & 544 & 1088 & 1632 & 2176 & 2720 & 3264 & 3808 & 4352 & 4896 & 5440\tabularnewline
+\hline
+69 & 28566 & 1104 & 2208 & 3312 & 4416 & 5520 & 6624 & 7728 & 8832 & 9936 & 11040\tabularnewline
+\hline
+70 & 29400 & 560 & 1120 & 1680 & 2240 & 2800 & 3360 & 3920 & 4480 & 5040 & 5600\tabularnewline
+\hline
+71 & 30246 & 1136 & 2272 & 3408 & 4544 & 5680 & 6816 & 7952 & 9088 & 10224 & 11360\tabularnewline
+\hline
+72 & 31104 & 576 & 1152 & 1728 & 2304 & 2880 & 3456 & 4032 & 4608 & 5184 & 5760\tabularnewline
+\hline
+73 & 31974 & 1168 & 2336 & 3504 & 4672 & 5840 & 7008 & 8176 & 9344 & 10512 & 11680\tabularnewline
+\hline
+74 & 32856 & 592 & 1184 & 1776 & 2368 & 2960 & 3552 & 4144 & 4736 & 5328 & 5920\tabularnewline
+\hline
+75 & 33750 & 1200 & 2400 & 3600 & 4800 & 6000 & 7200 & 8400 & 9600 & 10800 & 12000\tabularnewline
+\hline
+76 & 34656 & 608 & 1216 & 1824 & 2432 & 3040 & 3648 & 4256 & 4864 & 5472 & 6080\tabularnewline
+\hline
+77 & 35574 & 1232 & 2464 & 3696 & 4928 & 6160 & 7392 & 8624 & 9856 & 11088 & 12320\tabularnewline
+\hline
+78 & 36504 & 624 & 1248 & 1872 & 2496 & 3120 & 3744 & 4368 & 4992 & 5616 & 6240\tabularnewline
+\hline
+79 & 37446 & 1264 & 2528 & 3792 & 5056 & 6320 & 7584 & 8848 & 10112 & 11376 & 12640\tabularnewline
+\hline
+80 & 38400 & 640 & 1280 & 1920 & 2560 & 3200 & 3840 & 4480 & 5120 & 5760 & 6400\tabularnewline
+\hline
+81 & 39366 & 1296 & 2592 & 3888 & 5184 & 6480 & 7776 & 9072 & 10368 & 11664 & 12960\tabularnewline
+\hline
+82 & 40344 & 656 & 1312 & 1968 & 2624 & 3280 & 3936 & 4592 & 5248 & 5904 & 6560\tabularnewline
+\hline
+83 & 41334 & 1328 & 2656 & 3984 & 5312 & 6640 & 7968 & 9296 & 10624 & 11952 & 13280\tabularnewline
+\hline
+84 & 42336 & 672 & 1344 & 2016 & 2688 & 3360 & 4032 & 4704 & 5376 & 6048 & 6720\tabularnewline
+\hline
+85 & 43350 & 1360 & 2720 & 4080 & 5440 & 6800 & 8160 & 9520 & 10880 & 12240 & 13600\tabularnewline
+\hline
+86 & 44376 & 688 & 1376 & 2064 & 2752 & 3440 & 4128 & 4816 & 5504 & 6192 & 6880\tabularnewline
+\hline
+87 & 45414 & 1392 & 2784 & 4176 & 5568 & 6960 & 8352 & 9744 & 11136 & 12528 & 13920\tabularnewline
+\hline
+88 & 46464 & 704 & 1408 & 2112 & 2816 & 3520 & 4224 & 4928 & 5632 & 6336 & 7040\tabularnewline
+\hline
+89 & 47526 & 1424 & 2848 & 4272 & 5696 & 7120 & 8544 & 9968 & 11392 & 12816 & 14240\tabularnewline
+\hline
+90 & 48600 & 720 & 1440 & 2160 & 2880 & 3600 & 4320 & 5040 & 5760 & 6480 & 7200\tabularnewline
+\hline
+91 & 49686 & 1456 & 2912 & 4368 & 5824 & 7280 & 8736 & 10192 & 11648 & 13104 & 14560\tabularnewline
+\hline
+92 & 50784 & 736 & 1472 & 2208 & 2944 & 3680 & 4416 & 5152 & 5888 & 6624 & 7360\tabularnewline
+\hline
+93 & 51894 & 1488 & 2976 & 4464 & 5952 & 7440 & 8928 & 10416 & 11904 & 13392 & 14880\tabularnewline
+\hline
+94 & 53016 & 752 & 1504 & 2256 & 3008 & 3760 & 4512 & 5264 & 6016 & 6768 & 7520\tabularnewline
+\hline
+95 & 54150 & 1520 & 3040 & 4560 & 6080 & 7600 & 9120 & 10640 & 12160 & 13680 & 15200\tabularnewline
+\hline
+96 & 55296 & 768 & 1536 & 2304 & 3072 & 3840 & 4608 & 5376 & 6144 & 6912 & 7680\tabularnewline
+\hline
+97 & 56454 & 1552 & 3104 & 4656 & 6208 & 7760 & 9312 & 10864 & 12416 & 13968 & 15520\tabularnewline
+\hline
+98 & 57624 & 784 & 1568 & 2352 & 3136 & 3920 & 4704 & 5488 & 6272 & 7056 & 7840\tabularnewline
+\hline
+99 & 58806 & 1584 & 3168 & 4752 & 6336 & 7920 & 9504 & 11088 & 12672 & 14256 & 15840\tabularnewline
+\hline
+100 & 60000 & 800 & 1600 & 2400 & 3200 & 4000 & 4800 & 5600 & 6400 & 7200 & 8000\tabularnewline
+\hline
+101 & 61206 & 1616 & 3232 & 4848 & 6464 & 8080 & 9696 & 11312 & 12928 & 14544 & 16160\tabularnewline
+\hline
+102 & 62424 & 816 & 1632 & 2448 & 3264 & 4080 & 4896 & 5712 & 6528 & 7344 & 8160\tabularnewline
+\hline
+103 & 63654 & 1648 & 3296 & 4944 & 6592 & 8240 & 9888 & 11536 & 13184 & 14832 & 16480\tabularnewline
+\hline
+104 & 64896 & 832 & 1664 & 2496 & 3328 & 4160 & 4992 & 5824 & 6656 & 7488 & 8320\tabularnewline
+\hline
+105 & 66150 & 1680 & 3360 & 5040 & 6720 & 8400 & 10080 & 11760 & 13440 & 15120 & 16800\tabularnewline
+\hline
+106 & 67416 & 848 & 1696 & 2544 & 3392 & 4240 & 5088 & 5936 & 6784 & 7632 & 8480\tabularnewline
+\hline
+107 & 68694 & 1712 & 3424 & 5136 & 6848 & 8560 & 10272 & 11984 & 13696 & 15408 & 17120\tabularnewline
+\hline
+108 & 69984 & 864 & 1728 & 2592 & 3456 & 4320 & 5184 & 6048 & 6912 & 7776 & 8640\tabularnewline
+\hline
+109 & 71286 & 1744 & 3488 & 5232 & 6976 & 8720 & 10464 & 12208 & 13952 & 15696 & 17440\tabularnewline
+\hline
+110 & 72600 & 880 & 1760 & 2640 & 3520 & 4400 & 5280 & 6160 & 7040 & 7920 & 8800\tabularnewline
+\hline
+111 & 73926 & 1776 & 3552 & 5328 & 7104 & 8880 & 10656 & 12432 & 14208 & 15984 & 17760\tabularnewline
+\hline
+112 & 75264 & 896 & 1792 & 2688 & 3584 & 4480 & 5376 & 6272 & 7168 & 8064 & 8960\tabularnewline
+\hline
+113 & 76614 & 1808 & 3616 & 5424 & 7232 & 9040 & 10848 & 12656 & 14464 & 16272 & 18080\tabularnewline
+\hline
+114 & 77976 & 912 & 1824 & 2736 & 3648 & 4560 & 5472 & 6384 & 7296 & 8208 & 9120\tabularnewline
+\hline
+115 & 79350 & 1840 & 3680 & 5520 & 7360 & 9200 & 11040 & 12880 & 14720 & 16560 & 18400\tabularnewline
+\hline
+116 & 80736 & 928 & 1856 & 2784 & 3712 & 4640 & 5568 & 6496 & 7424 & 8352 & 9280\tabularnewline
+\hline
+117 & 82134 & 1872 & 3744 & 5616 & 7488 & 9360 & 11232 & 13104 & 14976 & 16848 & 18720\tabularnewline
+\hline
+118 & 83544 & 944 & 1888 & 2832 & 3776 & 4720 & 5664 & 6608 & 7552 & 8496 & 9440\tabularnewline
+\hline
+119 & 84966 & 1904 & 3808 & 5712 & 7616 & 9520 & 11424 & 13328 & 15232 & 17136 & 19040\tabularnewline
+\hline
+120 & 86400 & 960 & 1920 & 2880 & 3840 & 4800 & 5760 & 6720 & 7680 & 8640 & 9600\tabularnewline
+\hline
+121 & 87846 & 1936 & 3872 & 5808 & 7744 & 9680 & 11616 & 13552 & 15488 & 17424 & 19360\tabularnewline
+\hline
+122 & 89304 & 976 & 1952 & 2928 & 3904 & 4880 & 5856 & 6832 & 7808 & 8784 & 9760\tabularnewline
+\hline
+123 & 90774 & 1968 & 3936 & 5904 & 7872 & 9840 & 11808 & 13776 & 15744 & 17712 & 19680\tabularnewline
+\hline
+124 & 92256 & 992 & 1984 & 2976 & 3968 & 4960 & 5952 & 6944 & 7936 & 8928 & 9920\tabularnewline
+\hline
+125 & 93750 & 2000 & 4000 & 6000 & 8000 & 10000 & 12000 & 14000 & 16000 & 18000 & 20000\tabularnewline
+\hline
+126 & 95256 & 1008 & 2016 & 3024 & 4032 & 5040 & 6048 & 7056 & 8064 & 9072 & 10080\tabularnewline
+\hline
+127 & 96774 & 2032 & 4064 & 6096 & 8128 & 10160 & 12192 & 14224 & 16256 & 18288 & 20320\tabularnewline
+\hline
+128 & 98304 & 1024 & 2048 & 3072 & 4096 & 5120 & 6144 & 7168 & 8192 & 9216 & 10240\tabularnewline
+\hline
+129 & 99846 & 2064 & 4128 & 6192 & 8256 & 10320 & 12384 & 14448 & 16512 & 18576 & 20640\tabularnewline
+\hline
+\end{longtable}
+\par\end{center}
+
+\begin{center}
+%
+\begin{table}[H]
+\caption{Sample choices for $\nexxi$ given $\nprocxi$ based upon the relationship
+$\nexxi=8\times c\times\nprocxi$, where the integer $c\ge1$. The
+number of MPI slices, i.e., the total number of required processors,
+is $6\times\nprocxi^{2}$, as illustrated in Figure~\ref{figure:mpi_slices}.
+The approximate shortest period at which the global simulation is
+accurate for a given value of $\nexxi$ can be estimated by running
+the small serial program \texttt{xcreate\_header\_file}.}
+
+\end{table}
+
+\par\end{center}
+
+Finally, you 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}.
+This file is not used by the mesher or solver, but is required by
+the \texttt{go\_mesher} and \texttt{go\_solver} default job submission
+scripts. See Chapter \ref{cha:Running-Scheduler} for information
+about running the code on a system with a scheduler, e.g., LSF.
+
+Now that you have set the appropriate parameters in the \texttt{Par\_file}
+and have compiled the mesher, you are ready to launch it! This is
+most easily accomplished based upon the \texttt{go\_mesher} script.
+When you run on a PC cluster, the script assumes that the nodes are
+named n001, n002, etc. If this is not the case, change the \texttt{tr
+-d `n'} line in the script. You may also need to edit the last command
+at the end of the script that invokes the \texttt{mpirun} command.
+
+Mesher output is provided in the \texttt{OUTPUT\_FILES} directory
+in \texttt{output\_mesher.txt}; this file provides lots of details
+about the mesh that was generated. Alternatively, output can be directed
+to the screen instead by uncommenting a line in \texttt{constants.h}:
+
+\begin{lyxcode}
+!~uncomment~this~to~write~messages~to~the~screen~
+
+!~integer,~parameter~::~IMAIN~=~ISTANDARD\_OUTPUT~~
+\end{lyxcode}
+Note that on very fast machines, writing to the screen may slow down
+the code.
+
+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).
+
+Please note that it is difficult to correctly sample S waves in the
+inner core of the Earth because S-wave velocity is very small there.
+Therefore, correctly sampling S waves in the inner core would require
+a very dense mesh, which in turn would drastically reduce the time
+step of the explicit time scheme because the P wave velocity is very
+high in the inner core (Poisson's ratio is roughly equal to 0.44).
+Because shear wave attenuation is very high in the inner core ($Q_{\mu}$
+is approximately equal to 85), we have therefore decided to design
+the inner core mesh such that P waves are very well sampled but S
+waves are right at the sampling limit or even slightly below. This
+works fine because spurious numerical oscillations due to S-wave subsampling
+are almost completely suppressed by attenuation. However, this implies
+that one should not use SPECFEM3D\_GLOBE with the regular mesh and
+period estimates of Table \ref{table:nex} to study the PKJKP phase
+very precisely. If one is interested in that phase, one should use
+typically 1.5 times to twice the number of elements NEX indicated
+in the table.
+
+Regarding fluid/solid coupling at the CMB and ICB, in SPECFEM3D\_GLOBE
+we do not use the fluid-solid formulation of \citet{KoTr02a} and
+\citet{KoTr02b} anymore, we now use a displacement potential in the
+fluid (rather than a velocity potential as in \citet{KoTr02a} and
+\citet{KoTr02b}). This leads to the simpler fluid-solid matching
+condition introduced by \citet{ChVa04} with no numerical iterations
+at the CMB and ICB.
+
+For accuracy reasons, in the mesher the coordinates of the mesh points
+(arrays xstore, ystore and zstore) are always created in double precision.
+If the solver is compiled in single precision mode, the mesh coordinates
+are converted to single precision before being saved in the local
+mesh files.
+
+
+\section{Memory requirements}
+
+The SPECFEM3D\_GLOBE memory requirements can be estimated before or
+after running the mesher using the small serial program \texttt{\small xcreate\_header\_file},
+which reads the input file \texttt{\small DATA/Par\_file} and displays
+the total amount of memory that will be needed by the mesher and the
+solver to run it. This way, users can easily modify the parameters
+and check that their simulation will fit in memory on their machine.
+The file created by \texttt{\small xcreate\_header\_file} is called
+\texttt{OUTPUT\_FILES/values\_from\_mesher.h} and contains even more
+details about the future simulation.
+
+
+\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
+
+\begin{lyxcode}
+check\_buffers\_2D.f90
+
+check\_buffers\_1D.f90
+
+check\_buffers\_faces\_chunks.f90
+
+check\_buffers\_corners\_chunks.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. `\texttt{xcheck\_buffers\_1D}'
+checks the communication buffers between edges common to the mesh
+slices. `\texttt{xcheck\_buffers\_faces\_chunks}' checks the communication
+buffers between faces common to the mesh chunks, i.e., the faces of
+the six blocks of the cubed-sphere mesh. `\texttt{xcheck\_buffers\_corners\_chunks}'
+checks the communication buffers between edges common to the mesh
+chunks, which must be treated separately in MPI because they are of
+valence 3 (i.e., they are shared between three chunks).
+
+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
+the solver. For reasons of speed, the solver uses static memory allocation.
+Therefore it needs to be recompiled (type `\texttt{make clean}' and
+`\texttt{make specfem3D}') every time one reruns the mesher with different
+parameters. To compile the solver one needs a file generated by the
+mesher in the directory \texttt{OUTPUT\_FILES} called \texttt{values\_from\_mesher.h},
+which contains parameters describing the static size of the arrays
+as well as the setting of certain flags.
+
+The solver needs three input files in the \texttt{DATA} directory
+to run: the \texttt{Par\_file} that was discussed in detail in Chapter~\ref{cha:Running-the-Mesher},
+the earthquake source parameter file \texttt{CMTSOLUTION}, and the
+stations file \texttt{STATIONS}. Most parameters in the \texttt{Par\_file}
+should be set prior to running the mesher. Only the following parameters
+may be changed after running the mesher:
+
+\begin{itemize}
+\item the simulation type control parameters: \texttt{SIMULATION\_TYPE}
+and \texttt{SAVE\_FORWARD}
+\item the record length \texttt{RECORD\_LENGTH\_IN\_MINUTES}
+\item the movie control parameters \texttt{MOVIE\_SURFACE}, \texttt{MOVIE\_VOLUME},
+and \texttt{NTSTEPS\_BETWEEN\_FRAMES}
+\item the multi-stage simulation parameters \texttt{NUMBER\_OF\_RUNS} and
+\texttt{NUMBER\_OF\_THIS\_RUN}
+\item the output information parameters \texttt{NTSTEP\_BETWEEN\_OUTPUT\_INFO,
+NTSTEP\_BETWEEN\_OUTPUT\_}~\\
+\texttt{SEISMOS, OUTPUT\_SEISMOS\_ASCII\_TEXT, OUTPUT\_SEISMOS\_SAC\_ALPHANUM,
+OUTPUT\_}~\\
+\texttt{SEISMOS\_SAC\_BINARY and ROTATE\_SEISMOGRAMS\_RT}
+\item the \texttt{RECEIVERS\_CAN\_BE\_BURIED} and \texttt{PRINT\_SOURCE\_TIME\_FUNCTION}
+flags
+\end{itemize}
+Any other change to the \texttt{Par\_file} implies rerunning both
+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}.
+It looks like this:
+
+\begin{lyxcode}
+{\small }%
+\begin{figure}[H]
+\noindent \begin{centering}
+{\small \includegraphics[width=1\textwidth]{figures/Denali_CMT} }
+\par\end{centering}{\small \par}
+
+\caption{\texttt{CMTSOLUTION} file obtained from the Harvard CMT catalog. The
+top line is the initial estimate of the source, which is used as a
+starting point for the CMT solution. \textbf{M} is the moment tensor,
+$M_{0}${\small{} }is the seismic moment, and $M_{w}$ is the moment
+magnitude.}
+
+
+\label{fig:CMTSOLUTION-file}
+\end{figure}
+{\small \par}
+\end{lyxcode}
+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
+function, i.e., a moment-rate function that is a delta function. If
+\texttt{half duration} is not set to zero, the code will use a Gaussian
+(i.e., a signal with a shape similar to a `smoothed triangle', as
+explained in \citet{KoTr02a} and shown in Fig~\ref{fig:gauss.vs.triangle})
+source-time function with half-width \texttt{half duration}. We prefer
+to run the solver with \texttt{half duration} set to zero and convolve
+the resulting synthetic seismograms in post-processing after the run,
+because this way it is easy to use a variety of source-time functions
+(see Section \ref{sec:Process-data-and-syn}). \citet{KoTr02a} determined
+that the noise generated in the simulation by using a step source
+time function may be safely filtered out afterward based upon a convolution
+with the desired source time function and/or low-pass filtering. Use
+the postprocessing script \texttt{process\_syn.pl} (see Section \ref{sub:process_syn.pl})
+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
+
+\begin{lyxcode}
+make~convolve\_source\_timefunction
+\end{lyxcode}
+to compile the code and then set the parameter \texttt{hdur} in \texttt{UTILS/convolve\_source\_timefunction.csh}
+to the desired half-duration.
+
+\item The zero time of the simulation corresponds to the center of the triangle/Gaussian,
+or the centroid time of the earthquake. The start time of the simulation
+is $t=-1.5*\texttt{half duration}$ (the 1.5 is to make sure the moment
+rate function is very close to zero when starting the simulation).
+To convert to absolute time $t_{\mathrm{abs}}$, set
+
+\begin{lyxcode}
+$t_{\mathrm{abs}}=t_{\mathrm{pde}}+\texttt{time shift}+t_{\mathrm{synthetic}}$
+\end{lyxcode}
+where $t_{\mathrm{pde}}$ is the time given in the first line of the
+\texttt{CMTSOLUTION}, \texttt{time shift} is the corresponding value
+from the original \texttt{CMTSOLUTION} file and $t_{\mathrm{synthetic}}$
+is the time in the first column of the output seismogram.
+
+\end{itemize}
+%
+\begin{figure}
+\noindent \begin{centering}
+\includegraphics[width=3in]{figures/gauss_vs_triangle_mod}
+\par\end{centering}
+
+\caption{Comparison of the shape of a triangle and the Gaussian function actually
+used.}
+
+
+\label{fig:gauss.vs.triangle}
+\end{figure}
+
+
+Centroid latitude and longitude should be provided in geographical
+coordinates. The code converts these coordinates to geocentric coordinates~\citep{DaTr98}.
+Of course you may provide your own source representations by designing
+your own \texttt{CMTSOLUTION} file. Just make sure that the resulting
+file adheres to the Harvard CMT conventions (see Appendix~\ref{cha:Reference-Frame-Convention}).
+
+\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 $N_{\mathrm{sources}}$
+entries, one for each subevent (i.e., concatenate $N_{\mathrm{sources}}$
+\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,
+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}).
+
+Although it is convenient to think of each source as a triangle, in
+the simulation they are actually Gaussians (as they have better frequency
+characteristics). The relationship between the triangle and the Gaussian
+used is shown in Fig~\ref{fig:gauss.vs.triangle}. For finite fault
+simulations it is usually not advisable to use a zero half duration
+and convolve afterwards, since the half duration is generally fixed
+by the finite fault model.
+
+{\small }%
+\begin{figure}[H]
+\noindent \begin{centering}
+{\small \includegraphics[width=5in]{figures/source_timing} }
+\par\end{centering}{\small \par}
+
+\caption{Example of timing for three sources. The center of the first source
+triangle is defined to be time zero. Note that this is NOT in general
+the hypocentral time, or the start time of the source (marked as tstart).
+The parameter \texttt{time shift} in the \texttt{CMTSOLUTION} file
+would be t1(=0), t2, t3 in this case, and the parameter \texttt{half
+duration} would be hdur1, hdur2, hdur3 for the sources 1, 2, 3 respectively.}
+
+
+{\small \label{fig:source_timing} }
+\end{figure}
+{\small \par}
+
+The solver can calculate seismograms at any number of stations for
+basically the same numerical cost, so the user is encouraged to include
+as many stations as conceivably useful in the \texttt{STATIONS} file,
+which looks like this:
+
+{\small }%
+\begin{figure}[H]
+\noindent \begin{centering}
+{\small \includegraphics{figures/STATIONS_global_explained} }
+\par\end{centering}{\small \par}
+
+\caption{Sample \texttt{STATIONS} file. Station latitude and longitude should
+be provided in geographical coordinates. The width of the station
+label should be no more than 32 characters (see \texttt{MAX\_LENGTH\_STATION\_NAME}
+in the \texttt{constants.h} file), and the network label should be
+no more than 8 characters (see \texttt{MAX\_LENGTH\_NETWORK\_NAME}
+in the \texttt{constants.h} file).}
+
+\end{figure}
+{\small \par}
+
+Each line represents one station in the following format:
+
+\begin{lyxcode}
+\noindent {\small Station~Network~Latitude~(degrees)~Longitude~(degrees)~Elevation~(m)~burial~(m)~}{\small \par}
+\end{lyxcode}
+Solver output is provided in the \texttt{OUTPUT\_FILES} directory
+in the \texttt{output\_solver.txt} file. Output can be directed to
+the screen instead by uncommenting a line in \texttt{constants.h}:
+
+\begin{lyxcode}
+!~uncomment~this~to~write~messages~to~the~screen~
+
+!~integer,~parameter~::~IMAIN~=~ISTANDARD\_OUTPUT~
+\end{lyxcode}
+Note that on very fast machines, writing to the screen may slow down
+the code.
+
+While the solver is running, its progress may be tracked by monitoring
+the `\texttt{timestamp{*}}' files in the \texttt{OUTPUT\_FILES} directory.
+These tiny files look something like this:
+
+\begin{lyxcode}
+Time~step~\#~~~~~~~~~~~200~
+
+Time:~~~~0.6956667~~~~~~minutes~
+
+Elapsed~time~in~seconds~=~~~~~252.6748970000000~
+
+Elapsed~time~in~hh:mm:ss~=~~~~0~h~04~m~12~s~
+
+Mean~elapsed~time~per~time~step~in~seconds~=~~~~~1.263374485000000~
+
+Max~norm~displacement~vector~U~in~solid~in~all~slices~(m)~=~~~~1.9325~
+
+Max~non-dimensional~potential~Ufluid~in~fluid~in~all~slices~=~1.1058885E-22~
+\end{lyxcode}
+The \texttt{timestamp{*}} files provide the \texttt{Mean elapsed time
+per time step in seconds}, which may be used to assess performance
+on various machines (assuming you are the only user on a node), as
+well as the \texttt{\small Max}{\small{} }\texttt{\small norm}{\small{}
+}\texttt{\small displacement}{\small{} }\texttt{\small vector}{\small{}
+}\texttt{\small U}{\small{} }\texttt{\small in}{\small{} }\texttt{\small solid}{\small{}
+}\texttt{\small in}{\small{} }\texttt{\small all}{\small{} }\texttt{\small slices~(m)}{\small{}
+}\texttt{\small and}{\small{} }\texttt{\small Max}{\small{} }\texttt{\small non-dimensional}{\small{}
+}\texttt{\small potential}{\small{} }\texttt{\small Ufluid}{\small{}
+}\texttt{\small in}{\small{} }\texttt{\small fluid}{\small{} }\texttt{\small in}{\small{}
+}\texttt{\small all}{\small{} }\texttt{\small slices}. If something
+is wrong with the model, the mesh, or the source, you will see the
+code become unstable through exponentionally growing values of the
+displacement and/or fluid potential with time, and ultimately the
+run will be terminated by the program when either of these values
+becomes greater than \texttt{STABILITY\_THRESHOLD} defined in \texttt{constants.h}.
+You can control the rate at which the timestamp files are written
+based upon the parameter \texttt{NTSTEP\_BETWEEN\_OUTPUT\_INFO} in
+the \texttt{Par\_file}.
+
+Having set the \texttt{Par\_file} parameters, and having provided
+the \texttt{CMTSOLUTION} and \texttt{STATIONS} files, you are now
+ready to launch the solver! This is most easily accomplished based
+upon the \texttt{go\_solver} script (see Chapter~\ref{cha:Running-Scheduler}
+for information about running the code through a scheduler, e.g.,
+LSF). You may need to edit the last command at the end of the script
+that invokes the \texttt{mpirun} command. Another option is to use
+the \texttt{runall} script, which compiles and runs both mesher and
+solver in sequence. This is a safe approach that ensures using the
+correct combination of mesher output and solver input.
+
+It is important to realize that the CPU and memory requirements of
+the solver are closely tied to choices about attenuation (\texttt{ATTENUATION})
+and the nature of the model (i.e., isotropic models are cheaper than
+anisotropic models). We encourage you to run a variety of simulations
+with various flags turned on or off to develop a sense for what is
+involved.
+
+For the same model, one can rerun the solver for different events
+by simply changing the \texttt{CMTSOLUTION} file, and/or for different
+stations by changing the \texttt{STATIONS} file. There is no need
+to rerun the mesher. Of course it is best to include as many stations
+as possible, since this does not add significantly to the cost of
+the simulation.
+
+
+\chapter{\label{cha:Regional-Simulations}Regional Simulations}
+
+The code has the option of running in 1-, 2-, 3- or 6-chunk mode.
+The 1- or 2-chunk options may be used for higher resolution regional
+simulations. A one-chunk mesh may have lateral dimensions other than
+the customary $90^{\circ}$ per chunk, which can further increase
+the resolution of the mesh, and thus reduce the shortest period in
+the synthetic seismograms (but of course then also reducing the time
+step in order for the simulation to remain stable). A disadvantage
+of regional simulations is that one needs to use approximate absorbing
+boundary conditions on the side and bottom edges of the model (e.g.,
+see \citet{KoTr99} for a description of the paraxial boundary conditions
+used). Figure~\vref{fig:3D-spectral-element-mesh} and Figure~\vref{fig:Close-up-view-of}
+show an example of a one-chunk mesh centered on the Japan subduction
+zone, applied in the Japan regional waveform simulation \citep{ChTrHeKa07}.
+
+
+\section{One-Chunk Simulations\label{sec:One-Chunk-Simulations}}
+
+For a one-chunk regional simulation the following parameters need
+to be set in the \texttt{Par\_file}:
+
+\begin{description}
+\item [{$\nchunks$}] Must be set to 1.
+\item [{\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}}] Denotes the width of
+one side of the chunk ($90^{\circ}$or less).
+\item [{\texttt{ANGULAR\_WIDTH\_ETA\_IN\_DEGREES}}] Denotes the width of
+the second side of the chunk ($90^{\circ}$or less). Note that this
+value may be different from \texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}.
+\item [{\texttt{CENTER\_LATITUDE\_IN\_DEGREES}}] Defines the latitude of
+the center of the chunk (degrees).
+\item [{\texttt{CENTER\_LONGITUDE\_IN\_DEGREES}}] Defines the longitude
+of the center of the chunk (degrees).
+\item [{\texttt{GAMMA\_ROTATION\_AZIMUTH}}] Defines the rotation angle
+of the chunk about its center measured counter clockwise from due
+North (degrees). The corners of the mesh are output in \texttt{\small OUTPUT\_FILES/values\_from\_mesher.h}.
+The output corner progression in \texttt{\small OUTPUT\_FILES/values\_from\_mesher.h}
+is bottom left, bottom right, top left, top right. The rotation azimuth
+can be changed in the \texttt{Par\_file} and the corners output \texttt{(}\texttt{\small OUTPUT\_FILES/}~\\
+\texttt{\small values\_from\_mesher.h}\texttt{)} by using{\small{}
+}\texttt{\small xcreate\_header\_file}. It is important to note that
+the mesher or the solver does not need to be run to determine the
+limits of a 1-chunk simulation.
+\item [{$\nexxi$}] The number of spectral elements along the $\xi$ side
+of the chunk. This number \textit{must} be 8~$\times$~a multiple
+of $\nprocxi$ defined below. For a $90^{\circ}$ chunk, we do not
+recommend using $\nexxi$ less than~64 because the curvature of the
+Earth cannot be honored if one uses too few elements, which results
+in inaccurate and unstable simulations.
+\item [{$\nexeta$}] The number of spectral elements along the $\eta$
+side of the chunk. This number \textit{must} be 8~$\times$~a multiple
+of $\nproceta$ defined below. Note that in order to get elements
+that are close to square on the Earth's surface, the following ratios
+should be similar:
+
+\begin{lyxcode}
+$\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}/\nexxi$
+
+$\texttt{ANGULAR\_WIDTH\_ETA\_IN\_DEGREES}/\nexeta$~
+\end{lyxcode}
+Because of the geometry of the cubed sphere, the option of having
+different values for $\nexxi$ and $\nexeta$ is available only for
+regional simulations when $\nchunks=1$ (1/6th of the sphere).
+
+\item [{$\nprocxi$}] The number of processors or mesh slices along the
+$\xi$ side of the chunk. To accommodate the mesh doubling layers,
+we must have $\nexxi=8\times c\times\nprocxi$, where $c\ge1$ is
+a positive integer. See Table~\ref{table:nex} for various suitable
+choices.
+\item [{$\nproceta$}] The number of processors or slices along the $\eta$
+side of the chunk; we must have $\nexeta=8\times c\times\nproceta$,
+where $c\ge1$ is a positive integer. $\nprocxi$ and $\nproceta$
+must be equal when $\nchunks=6$.
+\end{description}
+%
+\begin{figure}[H]
+\begin{centering}
+\includegraphics[scale=0.65]{figures/fig5a}
+\par\end{centering}
+
+\caption{\textbf{\label{fig:3D-spectral-element-mesh}}S-wave velocity anomalies
+from the global tomographic model s20rts \citep{RiVa00} are superimposed
+on the mesh. For parallel computing purposes, the one-chunk SEM simulation
+is subdivided in terms of 64 slices. The center of the chunk is at
+(38.5$^{\circ}$ N, 137.5$^{\circ}$ E), and the lateral dimensions
+are 30$^{\circ}$ $\times$ 30$^{\circ}$. Two doubling layers are
+indicated at a depth of 25~km (PREM Moho depth) and a depth of about
+1650~km. Shows full view of 25 neighboring slices; see Figure~\ref{fig:Close-up-view-of}
+for close-up of upper mantle mesh.}
+
+\end{figure}
+%
+\begin{figure}[H]
+\begin{centering}
+\includegraphics[scale=0.65]{figures/fig5b}
+\par\end{centering}
+
+\caption{\textbf{\label{fig:Close-up-view-of}}Close-up view of the upper mantle
+mesh shown in Figure~\ref{fig:3D-spectral-element-mesh}. Note that
+the element size in the crust (top layer) is 13~km $\times$ 13~km,
+and that the size of the spectral elements is doubled in the upper
+mantle. The velocity variation is captured by NGLL = 5 grid points
+in each direction of the elements \citep{KoTr02a,KoTr02b}.}
+
+\end{figure}
+
+
+\begin{description}
+\item [{\texttt{ABSORBING\_CONDITIONS}}] Set to \texttt{.true.}{\small{}
+}for regional simulations. For instance, see \citet{KoTr99} for a
+description of the paraxial boundary conditions used. Note that these
+conditions are never perfect, and in particular surface waves may
+partially reflect off the artificial boundaries. Note also that certain
+arrivals, e.g., PKIKPPKIKP, will be missing from the synthetics.
+\end{description}
+When the width of the chunk is different from $90^{\circ}$ (or the
+number of elements is greater than 1248), the radial distribution
+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,
+the time stepping and period range in which the attenuation is applied
+is automatically determined. The minimum and maximum periods for attenuation
+are:
+
+\[
+\omega_{max}=\omega_{min}\times10^{W_{3}}\]
+
+
+\noindent where $W_{3}$ is the optimal width in frequency for 3 Standard
+Linear Solids, about 1.75. See \texttt{\small read\_compute\_parameters.f90}
+for more details.
+
+The time stepping is determined in a similar fashion as Equation (48)
+in \citet{KoTr02a}:
+
+\begin{lyxcode}
+dt~=~$S_{c}$~Element~Width~in~km~($r=$ICB)~/~Velocity~($r=$ICB)
+\end{lyxcode}
+where $S_{c}$ is the stability condition (about 0.4). We use the
+radius at the inner core boundary because this is where the maximum
+velocity/element width occurs. Again, see \texttt{\small read\_compute\_parameters}\texttt{.f90}
+for all the details.
+
+The approximate shortest period at which a regional simulation is
+accurate may be determined based upon the relation \begin{equation}
+\mbox{shortest period (s)}\simeq(256/\nexxi)\times(\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}/90)\times17.\label{eq:shortest_period_regional}\end{equation}
+
+
+
+\section{Two-Chunk Simulations}
+
+For a two-chunk regional simulation the following parameters need
+to be set in the \texttt{Par\_file}:
+
+\begin{description}
+\item [{$\nchunks$}] Must be set to 2
+\item [{\texttt{ANGULAR\_WIDTH\_XI\_IN\_DEGREES}}] Denotes the width of
+one side of the chunk, and it has to be 90 degrees.
+\item [{\texttt{ANGULAR\_WIDTH\_ETA\_IN\_DEGREES}}] Denotes the width of
+the second side of the chunk, and it also has to be 90 degrees.
+\end{description}
+\texttt{NEX\_XI} and \texttt{NEX\_ETA} follow the same description
+in Section \ref{sec:One-Chunk-Simulations}, however, they need to
+be the same in this case. All other parameters are similar to the
+one-chunk simulations, refer to Section \ref{sec:One-Chunk-Simulations}
+for details.
+
+%
+\begin{figure}[H]
+\noindent \begin{centering}
+\includegraphics[width=0.6\textwidth]{figures/2-chunk-surface}
+\par\end{centering}
+
+\caption{Geometry of a 2-chunk simulation, where the first chunk (\texttt{CHUNK\_AB})
+centers at $40^{\circ}$ latitude, $10^{\circ}$ longitude, and has
+been rotated by $20^{\circ}$ counter clockwise, and the second chunk
+(\texttt{CHUNK\_AC}) connects to the first chunk through one face.}
+
+\end{figure}
+
+
+
+\chapter{\label{cha:Adjoint-Simulations}Adjoint Simulations}
+
+Adjoint simulations are generally performed for two distinct applications.
+First, they can be used for earthquake source inversions, especially
+earthquakes with large ruptures such as the Sumatra-Andaman event
+\citep{LayKanamoriAmmon2005,AmmonJiThio2005,ParkSongTromp2005}. Second,
+they can be used to generate finite-frequency sensitivity kernels
+that are a critical part of tomographic inversions based upon 3D reference
+models \citep{trompetal2005,LiTr06,LiTr08}. In either case, source
+parameter or velocity structure updates are sought to minimize a specific
+misfit function (e.g., waveform or traveltime differences), and the
+adjoint simulation provides a means of computing the gradient of the
+misfit function and further reducing it in successive iterations.
+Applications and procedures pertaining to source studies and finite-frequency
+kernels are discussed in Sections~\ref{sec:Adjoint-simulation-sources}
+and \ref{sec:Adjoint-simulation-finite}, respectively. The two related
+parameters in the \texttt{Par\_file} are \texttt{SIMULATION\_TYPE}
+(1, 2 or 3) and \texttt{SAVE\_FORWARD} (boolean).
+
+
+\section{\label{sec:Adjoint-simulation-sources}Adjoint Simulations for Sources}
+
+In the case where a specific misfit function is minimized to invert
+for the earthquake source parameters, the gradient of the misfit function
+with respect to these source parameters can be computed by placing
+time-reversed seismograms at the receivers and using them as sources
+in an adjoint simulation, and then the value of the gradient is obtained
+from the adjoint seismograms recorded at the original earthquake location.
+
+\begin{enumerate}
+\item \textbf{Prepare the adjoint sources} \label{enu:Prepare-the-adjoint}
+
+\begin{enumerate}
+\item First, run a regular forward simlation (\texttt{SIMULATION\_TYPE =
+1} and \texttt{SAVE\_FORWARD = .false.}). You can automatically set
+these two variables using the \texttt{\small UTILS/change\_simulation\_type.pl}
+script:
+
+\begin{lyxcode}
+UTILS/change\_simulation\_type.pl~-f~
+\end{lyxcode}
+and then collect the recorded seismograms at all the stations given
+in \texttt{DATA/STATIONS}.
+
+\item Then select the stations for which you want to compute the time-reversed
+adjoint sources and run the adjoint simulation, and compile them into
+the \texttt{DATA/STATIONS\_ADJOINT} file, which has the same format
+as the regular \texttt{DATA/STATIONS} file.
+
+\begin{itemize}
+\item Depending on what type of misfit function is used for the source inversion,
+adjoint sources need to be computed from the original recorded seismograms
+for the selected stations and saved in the \texttt{SEM/} directory
+with the format \texttt{STA.NT.LH?.adj}, where \texttt{STA}, \texttt{NT}
+are the station name and network code given in the \texttt{DATA/STATIONS\_ADJOINT}
+file, and \texttt{LH?} represents the component name of a particular
+adjoint seismogram.
+\item The adjoint seismograms are in the same format as the original seismogram
+(\texttt{STA.NT.LH?.sem?}), with the same start time, time interval
+and record length.
+\end{itemize}
+\item Notice that even if you choose to time reverse only one component
+from one specific station, you still need to supply all three components
+because the code is expecting them (you can set the other two components
+to be zero).
+\item Also note that since time-reversal is done in the code itself, no
+explicit time-reversing is needed for the preparation of the adjoint
+sources, i.e., the adjoint sources are in the same forward time sense
+as the original recorded seismograms.
+\end{enumerate}
+\item \textbf{Set the related parameters and run the adjoint simulation}\\
+In the \texttt{DATA/Par\_file}, set the two related parameters to
+be \texttt{SIMULATION\_TYPE = 2} and \texttt{SAVE\_FORWARD = .false.}.
+More conveniently, use the scripts \texttt{UTILS/change\_simulation\_type.pl}
+to modify the \texttt{Par\_file} automatically (\texttt{change\_simulation\_type.pl
+-a}). Then run the solver to launch the adjoint simulation.
+\item \textbf{Collect the seismograms at the original source location}
+
+
+After the adjoint simulation has completed successfully, get the seismograms
+from directory \texttt{OUTPUT\_FILES}.
+
+\begin{itemize}
+\item These adjoint seismograms are recorded at the locations of the original
+earthquake sources given by the \texttt{DATA/CMTSOLUTION} file, and
+have names of the form \texttt{S?????.NT.S??.sem} for the six-component
+strain tensor (\texttt{SNN,SEE,SZZ,SNE,SNZ,SEZ}) at these locations,
+and \texttt{S?????.NT.LH?.sem} for the three-component displacements
+(\texttt{LHN,LHE,LHZ}) recorded at these locations.
+\item \texttt{S?????} denotes the source number; for example, if the original
+\texttt{CMTSOLUTION} provides only a point source, then the seismograms
+collected will start with \texttt{S00001}.
+\item These adjoint seismograms provide critical information for the computation
+of the gradient of the misfit function.
+\end{itemize}
+\end{enumerate}
+
+\section{\label{sec:Adjoint-simulation-finite}Adjoint Simulations for Finite-Frequency
+Kernels (Kernel Simulation)}
+
+Finite-frequency sensitivity kernels are computed in two successive
+simulations (please refer to \citet{LiTr06} for details).
+
+\begin{enumerate}
+\item \textbf{Run a forward simulation with the state variables saved at
+the end of the simulation}
+
+
+Prepare the \texttt{\small CMTSOLUTION} and \texttt{\small STATIONS}
+files, set the parameters \texttt{\small SIMULATION\_TYPE}{\small{}
+}\texttt{\small =}{\small{} }\texttt{\small 1} and \texttt{\small SAVE\_FORWARD
+=}{\small{} }\texttt{\small .true.} in the \texttt{Par\_file} (\texttt{change\_simulation\_type
+-F}), and run the solver.
+
+\begin{itemize}
+\item Notice that attenuation is not implemented yet for the computation
+of finite-frequency kernels; therefore set \texttt{ATTENUATION = .false.}
+in the \texttt{Par\_file}.
+\item We also suggest you modify the half duration of the \texttt{CMTSOLUTION}
+to be similar to the accuracy of the simulation (see Equation \ref{eq:shortest_period}
+or \ref{eq:shortest_period_regional}) to avoid too much high-frequency
+noise in the forward wavefield, although theoretically the high-frequency
+noise should be eliminated when convolved with an adjoint wavefield
+with the proper frequency content.
+\item This forward simulation differs from the regular simulations (\texttt{\small SIMULATION\_TYPE}{\small{}
+}\texttt{\small =}{\small{} }\texttt{\small 1} and \texttt{\small SAVE\_FORWARD}{\small{}
+}\texttt{\small =}{\small{} }\texttt{\small .false.}) described in
+the previous chapters in that the state variables for the last time
+step of the simulation, including wavefields of the displacement,
+velocity, acceleration, etc., are saved to the \texttt{LOCAL\_PATH}
+to be used for the subsequent simulation.
+\item For regional simulations, the files recording the absorbing boundary
+contribution are also written to the \texttt{LOCAL\_PATH} when \texttt{SAVE\_FORWARD
+= .true.}.
+\end{itemize}
+\item \textbf{Prepare the adjoint sources}
+
+
+The adjoint sources need to be prepared the same way as described
+in Section~\ref{sec:Adjoint-simulation-sources}, item~\ref{enu:Prepare-the-adjoint}.
+
+\begin{itemize}
+\item In the case of travel-time finite-frequency kernel for one source-receiver
+pair, i.e., point source from the \texttt{CMTSOLUTION}, and one station
+in the \texttt{STATIONS\_ADJOINT} list, we supply a sample program
+in \texttt{UTILS/cut\_velocity} to cut a certain portion of the original
+displacement seismograms and convert them into the proper adjoint
+source to compute the finite-frequency kernel.
+
+\begin{lyxcode}
+cut\_velocity~t1~t2~ifile{[}0-5]~E/N/Z-ascii-files~{[}baz]
+\end{lyxcode}
+where \texttt{t1} and \texttt{t2} are the start and end time of the
+portion you are interested in, \texttt{ifile} denotes the component
+of the seismograms to be used (0 for all three components, 1 for east,
+2 for north, and 3 for vertical, 4 for transverse, and 5 for radial
+component), \texttt{E/N/Z-ascii-files} indicate the three-component
+displacement seismograms in the right order, and \texttt{baz} is the
+back-azimuth of the station from the event location. Note that \texttt{baz}
+is only supplied when \texttt{ifile} = 4 or 5.
+
+\end{itemize}
+\item \textbf{Run the kernel simulation}
+
+
+With the successful forward simulation and the adjoint source ready
+in \texttt{SEM/}, set \texttt{SIMULATION\_TYPE = 3} and \texttt{SAVE\_FORWARD
+= .false.} in the \texttt{Par\_file(change\_simulation\_type.pl -b)},
+and rerun the solver.
+
+\begin{itemize}
+\item The adjoint simulation is launched together with the back reconstruction
+of the original forward wavefield from the state variables saved from
+the previous forward simulation, and the finite-frequency kernels
+are computed by the interaction of the reconstructed forward wavefield
+and the adjoint wavefield.
+\item The back-reconstructed seismograms at the original station locations
+are saved to the \texttt{OUTPUT\_FILES} directory at the end of the
+kernel simulations.
+\item These back-constructed seismograms can be compared with the time-reversed
+original seismograms to assess the accuracy of the backward reconstruction,
+and they should match very well (in the time-reversed sense).
+\item The files containing the density, P-wave speed and S-wave speed kernels
+are saved in the \texttt{LOCAL\_PATH} with the names of \texttt{proc??????\_reg\_?\_rho(alpha,beta)\_kernel.bin},
+where \texttt{proc??????} represents the processor number, and \texttt{reg\_?}
+denotes the region these kernels are for, including mantle (\texttt{reg\_1}),
+outer core (\texttt{reg\_2}), and inner core (\texttt{reg\_3}). The
+output kernels are in the unit of $s/km^{3}$.
+\end{itemize}
+\item \textbf{Run the boundary kernel simulation}
+
+
+\noindent If you set the \texttt{SAVE\_BOUNDARY\_MESH = .true.} in
+the \texttt{constants.h} file before the simulations, i.e., at the
+beginning of step 1, you will get not only the volumetric kernels
+as described in step 3, but also boundary kernels for the Earth's
+internal discontinuities, such as Moho, 410-km discontinuity, 670-km
+discontinuity, CMB and ICB. These kernel files are also saved in the
+local scratch directory defined by \texttt{LOCAL\_PATH }and have names
+such as \texttt{proc??????\_reg\_1(2)\_Moho(d400,d670,CMB,ICB)\_kernel.bin}.
+For a theoretical derivation of the boundary kernels, refer to \citet{trompetal2005},
+and for the visualization of the boundary kernels, refer to Section
+\ref{sec:Finite-Frequency-Kernels}.
+
+\item \textbf{Run the anisotropic kernel simulation}
+
+
+Instead of the kernels for the isotropic wave speeds, you can also
+compute the kernels for the 21 independent components $C_{IJ},\, I,J=1,...,6$
+(using Voigt's notation) of the elastic tensor in the (spherical)
+geographical coordinate system. This is done by setting \texttt{ANISOTROPIC\_KL}
+\texttt{=} \texttt{.true.} in \texttt{constants.h} before step 3.
+The definition of the parameters $C_{IJ}$ in terms of the corresponding
+components $c_{ijkl},ijkl,i,j,k,l=1,2,3$ of the elastic tensor in
+spherical coordinates follows \citet{ChTr07}. The computation of
+the anisotropic kernels is only implemented in the crust and mantle
+regions. The 21 anisotropic kernels are saved in the \texttt{LOCAL\_PATH}
+in one file with the name of \texttt{proc??????\_reg1\_cijkl\_kernel.bin}
+(with \texttt{proc??????} the processor number). The output kernels
+correspond to perturbation $\delta C_{IJ}$ of the elastic parameters
+and their unit is in $s/GPa/km^{3}$. For consistency, the output
+density kernels with this option turned on are for a perturbation
+$\delta\rho$ (and not $\frac{\delta\rho}{\rho}$) and their unit
+is in s / (kg/m$^{3}$) / km$^{3}$. These `primary' anisotropic kernels
+can then be combined to obtain the kernels related to other descriptions
+of anisotropy. This can be done, for example, when combining the kernel
+files from slices into one mesh file (see Section~\ref{sec:Finite-Frequency-Kernels}).
+
+\end{enumerate}
+In general, the first three steps need to be run sequentially to ensure
+proper access to the necessary files at different stages. If the simulations
+are run through some cluster scheduling system (e.g., LSF), and the
+forward simulation and the subsequent kernel simulations cannot be
+assigned to the same set of computer nodes, the kernel simulation
+will not be able to access the database files saved by the forward
+simulation. Solutions for this problem are provided in Chapter~\ref{cha:Running-Scheduler}.
+Visualization of the finite-frequency kernels is discussed in Section~\ref{sec:Finite-Frequency-Kernels}.
+
+
+\chapter{Graphics}
+
+
+\section{\label{sec:Meshes}Meshes}
+
+Use the serial code \texttt{combine\_AVS\_DX.f90} (type `\texttt{make
+combine\_AVS\_DX}' and then `\texttt{xcombine\_AVS\_DX}') to generate
+AVS \url{www.avs.com} output files (in AVS UCD format) or OpenDX \url{www.opendx.org}
+output files showing the mesh, the MPI partition (slices), the $\nchunks$
+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})
+for reference.
+
+
+\section{\label{sec:Movies}Movies}
+
+To make a surface or volume movie of the simulation, set parameters
+\texttt{MOVIE\_SURFACE}, \texttt{MOVIE\_VOLUME}, and \texttt{NTSTEP\_BETWEEN\_FRAMES}
+in the \texttt{Par\_file}. Turning on the movie flags, in particular
+\texttt{MOVIE\_VOLUME}, produces large output files. \texttt{MOVIE\_VOLUME}
+files are saved in the \texttt{LOCAL\_PATH} directory, whereas \texttt{MOVIE\_SURFACE}
+output files are saved in the \texttt{OUTPUT\_FILES} directory. We
+save the velocity field. The look of a movie is determined by the
+half-duration of the source. The half-duration should be large enough
+so that the movie does not contain frequencies that are not resolved
+by the mesh, i.e., it should not contain numerical noise. This can
+be accomplished by selecting a CMT \texttt{HALF\_DURATION} > 1.1 $\times$
+smallest period (see figure \ref{fig:CMTSOLUTION-file}). When \texttt{\small MOVIE\_SURFACE}
+= \texttt{\small .true.} or \texttt{\small MOVIE\_VOLUME}{\small{}
+}\texttt{\small =}{\small{} }\texttt{\small .true.}, the half duration
+of each source in the \texttt{CMTSOLUTION} file is replaced by
+
+\begin{quote}
+\[
+\sqrt{(}\mathrm{\mathtt{HALF\_DURATIO}\mathtt{N}^{2}}+\mathrm{\mathtt{HDUR\_MOVI}\mathtt{E}^{2}})\]
+\textbf{NOTE:} If \texttt{HDUR\_MOVIE} is set to 0.0, the code will
+select the appropriate value of 1.1 $\times$ smallest period. As
+usual, for a point source one can set \texttt{HALF\_DURATION} in the
+\texttt{Par\_file} to be 0.0 and \texttt{HDUR\_MOVIE} = 0.0 to get
+the highest frequencies resolved by the simulation, but for a finite
+source one would keep all the \texttt{HALF\_DURATION}s as prescribed
+by the finite source model and set \texttt{HDUR\_MOVIE} = 0.0.
+\end{quote}
+
+\subsection{Movie Surface}
+
+When running \texttt{xspecfem3D} with the \texttt{MOVIE\_SURFACE}
+flag turned on the code outputs \texttt{moviedata??????} files in
+the \texttt{OUTPUT\_FILES} directory. The files are in a fairly complicated
+binary format, but there are two programs provided to convert the
+output into more user friendly formats. The first one, \texttt{create\_movie\_AVS\_DX.f90}
+outputs data in ASCII, OpenDX, AVS, or ParaView format. Run the code
+from the source directory (type `\texttt{make} \texttt{create\_movie\_AVS\_DX}'
+first) to create an input file in your format of choice. The code
+will prompt the user for input parameters. The second program \texttt{create\_movie\_GMT\_global.f90}
+outputs ASCII xyz files, convenient for use with GMT. This codes uses
+significantly less memory than \texttt{create\_movie\_AVS\_DX.f90}
+and is therefore useful for high resolution runs.
+
+%
+\begin{figure}[H]
+\noindent \begin{centering}
+\includegraphics[scale=0.75]{figures/geo-poster4_small}
+\par\end{centering}
+
+\caption{Snapshots from a global movie for the December 26, 2004, M=9.2 Sumatra-Andaman
+earthquake. Time runs down successive columns.}
+
+\end{figure}
+
+
+
+\subsection{\label{sub:Movie-Volume}Movie Volume}
+
+When running xspecfem3D with the \texttt{\small MOVIE\_VOLUME} flag
+turned on, the code outputs several files in \texttt{\small LOCAL\_DIR}.
+As the files can be very large, there are several flags in the \texttt{\small Par\_file}
+that control the region in space and time that is saved. These are:
+\texttt{\small MOVIE\_TOP\_KM}, \texttt{\small MOVIE\_BOTTOM\_KM},
+\texttt{\small MOVIE\_WEST\_DEG}, \texttt{\small MOVIE\_EAST\_DEG},
+\texttt{\small MOVIE\_NORTH\_DEG}, \texttt{\small MOVIE\_SOUTH\_DEG},
+\texttt{\small MOVIE\_START} and \texttt{\small MOVIE\_STOP}. The
+code will save a given element if the center of the element is in
+the prescribed volume.
+
+\begin{description}
+\item [{The~Top/Bottom:}] Depth below the surface in kilometers, use \texttt{\small MOVIE\_TOP}
+\texttt{\small =} \texttt{\small -100.0} to make sure the surface
+is stored.
+\item [{West/East:}] Longitude, degrees East {[}-180.0/180.0]
+\item [{North/South:}] Latitute, degrees North {[}-90.0/90.0]
+\item [{Start/Stop:}] Frames will be stored at \texttt{\small MOVIE\_START}
+\texttt{\small +} \texttt{\small i{*}NSTEP\_BETWEEN\_FRAMES}, where
+\texttt{\small i=(0,1,2..)} while \texttt{\small i{*}NSTEP\_BETWEEN\_FRAMES}
+\texttt{\small <=} \texttt{\small MOVIE\_STOP}{\small \par}
+\end{description}
+The code saves several files, and the output is saved by each processor.
+The first is \texttt{\small proc??????\_movie3D\_info.txt} which contains
+two numbers, first the number of points within the prescribed volume
+within this particular slice, and second the number of elements. The
+next files are \texttt{\small proc??????\_movie3D\_x.bin}, \texttt{\small proc??????\_movie3D\_y.bin},
+\texttt{\small proc??????\_movie3D\_z.bin} which store the locations
+of the points in the 3D mesh.
+
+Finally the code stores the ``value'' at each of the points. Which
+value is determined by \texttt{\small MOVIE\_VOLUME\_TYPE} in the
+\texttt{\small Par\_file}. Choose 1 to save the strain, 2 to save
+the time integral of strain, and 3 to save $\mu${*}time integral
+of strain in the subvolume. Choosing 4 causes the code to save the
+trace of the stress and the deviatoric stress in the whole volume
+(not the subvolume in space), at the time steps specified. The name
+of the output file will depend on the \texttt{\small MOVIE\_VOLUME\_TYPE}
+chosen.
+
+Setting \texttt{\small MOVIE\_VOLUME\_COARSE} \texttt{\small =} \texttt{\small .true.}
+will make the code save only the corners of the elements, not all
+the points within each element for \texttt{\small MOVIE\_VOLUME\_TYPE}
+\texttt{\small =} \texttt{\small 1,2,3}.
+
+To make the code output your favorite ``value'' simply add a new \texttt{\small MOVIE\_VOLUME\_TYPE},
+a new subroutine to \texttt{\small write\_movie\_volume.f90} and a
+subroutine call to \texttt{\small specfem3D.f90}.
+
+A utility program to combine the files produced by \texttt{\small MOVIE\_VOLUME\_TYPE}
+\texttt{\small =} \texttt{\small 1,2,3} is provided in \texttt{\small combine\_paraview}~\\
+\texttt{\small \_strain\_data.f90}. Type \texttt{\small xcombine\_paraview\_strain\_data}
+to get the usage statement. The program \texttt{\small combine\_vol}~\\
+\texttt{\small \_data.f90} can be used for \texttt{\small MOVIE\_VOLUME\_TYPE}
+\texttt{\small =} \texttt{\small 4}.
+
+
+\section{\label{sec:Finite-Frequency-Kernels}Finite-Frequency Kernels}
+
+The finite-frequency kernels computed as explained in Section \ref{sec:Adjoint-simulation-finite}
+are saved in the \texttt{LOCAL\_PATH} at the end of the simulation.
+Therefore, we first need to collect these files on the front end,
+combine them into one mesh file, and visualize them with some auxilliary
+programs.
+
+\begin{enumerate}
+\item \textbf{Create slice files}
+
+
+We will only discuss the case of one source-receiver pair, i.e., the
+so-called banana-doughnut kernels. Although it is possible to collect
+the kernel files from all slices onto the front end, it usually takes
+up too much storage space (at least tens of gigabytes). Since the
+sensitivity kernels are the strongest along the source-receiver great
+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
+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
+}directory. Then copy the \texttt{CMTSOLUTION} file, \texttt{STATIONS\_ADJOINT},
+and \texttt{Par\_file}, and run:
+
+\begin{lyxcode}
+global\_slice\_number.pl~CMTSOLUTION~STATIONS\_ADJOINT~Par\_file
+\end{lyxcode}
+In the case of visualization boundary kernels or spherical cross-sections
+of the volumetric kernels, it is necessary to obtain the slice numbers
+that cover a belt along the source and receiver great circle path,
+and you can use the hybrid version:
+
+\begin{lyxcode}
+globe\_slice\_number2.pl~CMTSOLUTION~STATIONS\_ADJOINT~
+
+~~~~~Par\_file~belt\_width\_in\_degrees
+\end{lyxcode}
+A typical value for \texttt{belt\_width\_in\_degrees} can be 20.
+
+\item For a full 6-chunk simulation, this script will generate the \texttt{slice\_minor},
+\texttt{slice\_major}, \texttt{slice\_ic} files, but for a one- or
+two-chunk simulation, this script only generates the \texttt{slice\_minor}
+file.
+\item For cases with multiple sources and multiple receivers, you need to
+provide a slice file before proceeding to the next step.
+\end{enumerate}
+\item \textbf{Collect the kernel files}
+
+
+After obtaining the slice files, you can collect the corresponding
+kernel files from the given slices.
+
+\begin{enumerate}
+\item To accomplish this, you can use or modify the scripts in \texttt{UTILS/collect\_database
+}directory:
+
+\begin{lyxcode}
+{\small copy\_m(oc,ic)\_globe\_database.pl~slice\_file~lsf\_machine\_file~filename~{[}jobid]}{\small \par}
+\end{lyxcode}
+for volumetric kernels, where \texttt{\small lsf\_machine\_file} is
+the machine file generated by the LSF scheduler, \texttt{\small filename}
+is the kernel name (e.g., \texttt{\small rho\_kernel}, \texttt{\small alpha\_kernel}
+and \texttt{\small beta\_kernel}), and the optional \texttt{\small jobid}
+is the name of the subdirectory under \texttt{\small LOCAL\_PATH}
+where all the kernel files are stored. For boundary kernels, you need
+to use
+
+\begin{lyxcode}
+{\small copy\_surf\_globe\_database.pl~slice\_file~lsf\_machine\_file~filename~{[}jobid]}{\small \par}
+\end{lyxcode}
+where the filename can be \texttt{\small Moho\_kernel}, \texttt{\small d400\_kernel},
+\texttt{\small d670\_kernel}, \texttt{\small CMB\_kernel} and \texttt{\small ICB\_kernel}.
+
+\item After executing this script, all the necessary mesh topology files
+as well as the kernel array files are collected to the local directory
+on the front end.
+\end{enumerate}
+\item \textbf{Combine kernel files into one mesh file}
+
+
+We use an auxilliary program \texttt{combine\_vol\_data.f90} to combine
+the volumetric kernel files from all slices into one mesh file, and
+\texttt{combine\_surf\_data.f90 }to combine the surface kernel files.
+
+\begin{enumerate}
+\item Compile it in the global code directory:
+
+\begin{lyxcode}
+{\footnotesize make~combine\_vol\_data~}{\footnotesize \par}
+
+{\footnotesize xcombine\_vol\_data}~{\footnotesize slice\_list}~{\footnotesize filename}~{\footnotesize input\_dir}~{\footnotesize output\_dir}~{\footnotesize high/low-resolution}~{\footnotesize {[}region]}{\footnotesize \par}
+\end{lyxcode}
+where \texttt{input\_dir} is the directory where all the individual
+kernel files are stored, and \texttt{output\_dir} is where the mesh
+file will be written.
+
+\begin{lyxcode}
+{\footnotesize xcombine\_surf\_data~slice\_list~filename~surfname~input\_dir~output\_dir~hi~gh/low-resolution~2D/3D}{\footnotesize \par}
+\end{lyxcode}
+where \texttt{surfname} should correspond to the specific kernel file
+name, and can be chosen from \texttt{Moho}, \texttt{400}, \texttt{670},
+\texttt{CMB} and \texttt{ICB}.
+
+\item Use 1 for a high-resolution mesh, outputting all the GLL points to
+the mesh file, or use 0 for low resolution, outputting only the corner
+points of the elements to the mesh file. Use 0 for 2D surface kernel
+files and 1 for 3D volumetric kernel files.
+\item Use region = 1 for the mantle, region =2 for the outer core, region
+= 3 for the inner core, and region = 0 for all regions.
+\item The output mesh file will have the name \texttt{reg\_?\_rho(alpha,beta)\_kernel.mesh,}
+or\texttt{ }~\\
+\texttt{reg\_?\_Moho(d400,d670,CMB,ICB)\_kernel.surf.}
+\end{enumerate}
+\item \textbf{Convert mesh files into .vtu files}
+
+\begin{enumerate}
+\item We next convert the \texttt{.mesh} file into the VTU (Unstructured
+grid file) format which can be viewed in ParaView, for example:
+
+\begin{lyxcode}
+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
+VTK \url{www.vtk.org} run-time library for its execution. Therefore,
+make sure you have them properly set in the script.
+\end{enumerate}
+\item \textbf{Copy over the source and receiver .vtk file}
+
+
+In the case of a single source and a single receiver, the simulation
+also generates the \texttt{OUTPUT\_FILES/sr.vtk} file to describe
+the source and receiver locations, which can be viewed in Paraview
+in the next step.
+
+\item \textbf{View the mesh in ParaView}
+
+
+Finally, we can view the mesh in ParaView \url{www.paraview.org}.
+
+\begin{enumerate}
+\item Open ParaView.
+\item From the top menu, \textsf{File} $\rightarrow$\textsf{ Open data},
+select \texttt{file.vtu}, and click the \textsf{Accept} button.
+
+\begin{itemize}
+\item If the mesh file is of moderate size, it shows up on the screen; otherwise,
+only the outline is shown.
+\end{itemize}
+\item Click \textsf{Display Tab} $\rightarrow$ \textsf{Display Style} $\rightarrow$
+\textsf{Representation} and select \textsf{wireframe of surface} to
+display it.
+\item To create a cross-section of the volumetric mesh, choose \textsf{Filter}
+$\rightarrow$ \textsf{cut}, and under \textsf{Parameters Tab}, choose
+\textsf{Cut Function} $\rightarrow$ \textsf{plane}.
+\item Fill in center and normal information given by the standard output
+from \texttt{global\_slice\_number.pl} script.
+\item To change the color scale, go to \textsf{Display Tab} $\rightarrow$
+\textsf{Color} $\rightarrow$ \textsf{Edit Color Map} and reselect
+lower and upper limits, or change the color scheme.
+\item Now load in the source and receiver location file by \textsf{File}
+$\rightarrow$\textsf{ Open data}, select \texttt{sr.vt}k, and click
+the \textsf{Accept} button. Choose \textsf{Filter} $\rightarrow$\textsf{
+Glyph}, and represent the points by `\textsf{spheres}'.
+\item For more information about ParaView, see the ParaView Users Guide \url{www.paraview.org/files/v1.6/ParaViewUsersGuide.PDF}.
+\end{enumerate}
+\end{enumerate}
+For illustration purposes, Figure \ref{fig:P-wave-speed-finite-frequency}
+shows the P-wave speed finite-frequency kernel for a P arrival recorded
+at an epicental distance of $60^{\circ}$ for a deep event.
+
+%
+\begin{figure}[H]
+\includegraphics[clip,scale=0.9]{figures/P_alpha_60d_18s}
+
+\caption{\label{fig:P-wave-speed-finite-frequency}P-wave speed finite-frequency
+kernel for a P arrival recorded at an epicentral distance of $60^{\circ}$.}
+
+\end{figure}
+
+
+
+\chapter{\label{cha:Running-Scheduler}Running through a Scheduler}
+
+The code is usually run on large parallel machines, often PC clusters,
+most of which use schedulers, i.e., queuing or batch management systems
+to manage the running of jobs from a large number of users. The following
+considerations need to be taken into account when running on a system
+that uses a scheduler:
+
+\begin{itemize}
+\item The processors/nodes to be used for each run are assigned dynamically
+by the scheduler, based on availability. Therefore, in order for the
+mesher and the solver (or between successive runs of the solver) to
+have access to the same database files (if they are stored on hard
+drives local to the nodes on which the code is run), they must be
+launched in sequence as a single job.
+\item On some systems, the nodes to which running jobs are assigned are
+not configured for compilation. It may therefore be necessary to pre-compile
+both the mesher and the solver. A small program provided in the distribution
+called \texttt{\small create\_header\_file.f90} can be used to directly
+create\texttt{\small{} OUTPUT\_FILES/values\_from\_mesher.h} using
+the information in the \texttt{\small DATA/Par\_file} without having
+to run the mesher (type \texttt{\small `make}{\small{} }\texttt{\small create\_header\_}~\\
+\texttt{\small file}' to compile it and `\texttt{\small xcreate\_header\_file}'
+to run it; refer to the sample scripts below). The solver can now
+be compiled as explained above.
+\item One feature of schedulers/queuing systems is that they allow submission
+of multiple jobs in a {}``launch and forget'' mode. In order to
+take advantage of this property, care needs to be taken that output
+and intermediate files from separate jobs do not overwrite each other,
+or otherwise interfere with other running jobs.
+\end{itemize}
+We describe here in some detail a job submission procedure for the
+Caltech 1024-node cluster, CITerra, under the LSF scheduling system.
+We consider the submission of a regular forward simulation. The two
+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/}
+directory and can straightforwardly be modified and adapted to meet
+more specific running needs.
+
+
+\section{\texttt{run\_lsf.bash}}
+
+This script first sets the job queue to be `normal'. It then compiles
+the mesher and solver together, figures out the number of processors
+required for this simulation from \texttt{DATA/Par\_file}, and submits
+the LSF job.
+
+\begin{lyxcode}
+\#!/bin/bash
+
+\#~use~the~normal~queue~unless~otherwise~directed~queue=\char`\"{}-q~normal\char`\"{}~
+
+if~{[}~\$\#~-eq~1~];~then
+
+~~~~~~~~echo~\char`\"{}Setting~the~queue~to~\$1\char`\"{}
+
+~~~~~~~~queue=\char`\"{}-q~\$1\char`\"{}~
+
+fi~\\
+~\\
+\#~compile~the~mesher~and~the~solver~
+
+d=`date'~echo~\char`\"{}Starting~compilation~\$d\char`\"{}~
+
+make~clean~
+
+make~meshfem3D~
+
+make~create\_header\_file~
+
+xcreate\_header\_file~
+
+make~specfem3D~
+
+d=`date'~
+
+echo~\char`\"{}Finished~compilation~\$d\char`\"{}~\\
+~\\
+\#~compute~total~number~of~nodes~needed~
+
+NPROC\_XI=`grep~NPROC\_XI~DATA/Par\_file~|~cut~-c~34-~'~
+
+NPROC\_ETA=`grep~NPROC\_ETA~DATA/Par\_file~|~cut~-c~34-~'~
+
+NCHUNKS=`grep~NCHUNKS~DATA/Par\_file~|~cut~-c~34-~'~\\
+~\\
+\#~total~number~of~nodes~is~the~product~of~the~values~read~
+
+numnodes=\$((~\$NCHUNKS~{*}~\$NPROC\_XI~{*}~\$NPROC\_ETA~))~\\
+~\\
+echo~\char`\"{}Submitting~job\char`\"{}~
+
+bsub~\$queue~-n~\$numnodes~-W~60~-K~<go\_mesher\_solver\_lsf\_globe.bash~
+\end{lyxcode}
+
+\section{\texttt{go\_mesher\_solver\_lsf\_globe.bash}}
+
+This script describes the job itself, including setup steps that can
+only be done once the scheduler has assigned a job-ID and a set of
+compute nodes to the job, the \texttt{run\_lsf.bash} commands used
+to run the mesher and the solver, and calls to scripts that collect
+the output seismograms from the compute nodes and perform clean-up
+operations.
+
+\begin{enumerate}
+\item First the script directs the scheduler to save its own output and
+output from \texttt{stdout} into \texttt{\small OUTPUT\_FILES/\%J.o},
+where \texttt{\%J} is short-hand for the job-ID; it also tells the
+scheduler what version of \texttt{mpich} to use (\texttt{mpich\_gm})
+and how to name this job (\texttt{go\_mesher\_solver\_lsf}).
+\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
+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
+are created using \texttt{shmux}, a shell multiplexor that can execute
+the same commands on many hosts in parallel. \texttt{shmux} is available
+from Shmux \url{web.taranis.org/shmux/}. Make sure that the \texttt{LOCAL\_PATH}
+parameter in \texttt{DATA/Par\_file} is also set properly.
+\item The next portion of the script launches the mesher and then the solver
+using \texttt{run\_lsf.bash}.
+\item The final portion of the script performs clean up on the nodes using
+the Perl script \texttt{cleanmulti.pl}
+\end{enumerate}
+\begin{lyxcode}
+\#!/bin/bash~-v
+
+\#BSUB~-o~OUTPUT\_FILES/\%J.o
+
+\#BSUB~-a~mpich\_gm
+
+\#BSUB~-J~go\_mesher\_solver\_lsf
+
+BASEMPIDIR=/scratch/\$USER/DATABASES\_MPI
+
+echo~\char`\"{}\$LSB\_MCPU\_HOSTS\char`\"{}~>~OUTPUT\_FILES/lsf\_machines
+
+echo~\char`\"{}\$LSB\_JOBID\char`\"{}~>~OUTPUT\_FILES/jobid
+
+./remap\_lsf\_machines.pl~OUTPUT\_FILES/lsf\_machines~>OUTPUT\_FILES/machines
+
+\#~Modif~:~create~a~directory~for~this~job
+
+shmux~-M50~-Sall~-c~\char`\"{}mkdir~-p~/scratch/\$USER;
+
+mkdir~-p~\$BASEMPIDIR.\$LSB\_JOBID\char`\"{}~-~<~OUTPUT\_FILES/machines~>/dev/null
+
+\#~Set~the~local~path~in~Par\_file
+
+sed~-e~\char`\"{}s:\textasciicircum{}LOCAL\_PATH~.{*}:LOCAL\_PATH~=~\$BASEMPIDIR.\$LSB\_JOBID:\char`\"{}
+
+<~DATA/Par\_file~>~DATA/Par\_file.tmp
+
+mv~DATA/Par\_file.tmp~DATA/Par\_file
+
+current\_pwd=\$PWD
+
+mpirun.lsf~~-{}-gm-no-shmem~-{}-gm-copy-env~\$current\_pwd/xmeshfem3D
+
+mpirun.lsf~-{}-gm-no-shmem~-{}-gm-copy-env~\$current\_pwd/xspecfem3D
+
+\#~clean~up
+
+cleanbase\_jobid.pl~OUTPUT\_FILES/machines~DATA/Par\_file
+\end{lyxcode}
+
+\section{\texttt{run\_lsf.kernel} and \texttt{go\_mesher\_solver\_globe.kernel}}
+
+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
+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
+in.
+
+
+\chapter{{\normalsize \label{cha:-Changing-the}} Changing the Model}
+
+In this section we explain how to change the crustal, mantle, or inner
+core models. These changes involve contributing specific subroutines
+that replace existing subroutines in the \texttt{SPECFEM3D\_GLOBE}
+package.
+
+
+\section{{\normalsize \label{sec:Changing-the-Crustal}}Changing the Crustal
+Model}
+
+The 3D crustal model Crust2.0 \citep{BaLaMa00} is superimposed onto
+the mesh by the subroutine \texttt{crustal\_model}~\\
+\texttt{.f90}. To accomplish this, the flag \texttt{CRUSTAL}, set
+in the subroutine \texttt{read\_compute\_parameters.f90}, is used
+to indicate a 3D crustal model. When this flag is set to \texttt{.true.},
+the crust on top of the 1D reference model (PREM, IASP91, or AK135)
+is removed and replaced by extending the mantle. The 3D crustal model
+is subsequently overprinted onto the crust-less 1D reference model.
+The call to the 3D crustal routine is of the form
+
+\begin{lyxcode}
+call~crustal\_model(lat,lon,r,vp,vs,rho,moho,foundcrust,CM\_V)
+\end{lyxcode}
+Input to this routine consists of:
+
+\begin{description}
+\item [{\texttt{lat}}] Latitude in degrees.
+\item [{\texttt{lon}}] Longitude in degrees.
+\item [{\texttt{r}}] Non-dimensionalized radius ($0<\texttt{r}<1$).
+\end{description}
+Output from the routine consists of:
+
+\begin{description}
+\item [{\texttt{vp}}] Non-dimensionalized compressional wave speed at location
+(\texttt{lat},\texttt{lon},\texttt{r}).
+\item [{\texttt{vs}}] Non-dimensionalized shear wave speed.
+\item [{\texttt{rho}}] Non-dimensionalized density.
+\item [{\texttt{moho}}] Non-dimensionalized Moho depth.
+\item [{\texttt{found\_crust}}] Logical that is set to \texttt{.true.}
+only if crust exists at location (\texttt{lat},\texttt{lon},\texttt{r}),
+i.e., \texttt{.false.} for radii \texttt{r} in the mantle. This flags
+determines whether or not a particular location is in the crust and,
+if so, what parameters to assign to the mesh at this location.
+\item [{\texttt{CM\_V}}] Fortran structure that contains the parameters,
+variables and arrays that describe the model.
+\end{description}
+All output needs to be non-dimensionalized according to the convention
+summarized in Appendix~\ref{cha:Non-Dimensionalization-Conventions}.
+You can replace this subroutine by your own routine \textit{provided
+you do not change the call structure of the routine}, i.e., the new
+routine should take exactly the same input and produce the required,
+properly non-dimensionalized output.
+
+Part of the file \texttt{crustal\_model.f90} is the subroutine \texttt{read\_crustal\_model}.
+The call to this routine takes argument \texttt{CM\_V} and is used
+to once-and-for-all read in the databases related to Crust2.0. If
+you replace the file \texttt{crustal\_model.f90} with your own implementation,
+you \textit{must} provide a \texttt{read\_crustal\_model} routine,
+even if it does nothing. Model constants and variables read by the
+routine \texttt{read\_crustal\_model} are passed to the subroutine
+\texttt{read\_crustal\_model} through the structure \texttt{CM\_V}.
+An alternative crustal model should use the same construct. Please
+feel free to contribute subroutines for new models and send them to
+us so that they can be included in future releases of the software.
+
+\begin{quote}
+\textbf{NOTE:} If you decide to create your own version of file \texttt{crustal\_model.f90},
+you must add calls to \texttt{MPI\_BCAST} in file \texttt{meshfem3D.f90}
+after the call to the \texttt{read\_crustal\_model} subroutine that
+reads the isotropic mantle model once and for all in the mesher. This
+is done in order to read the (potentially large) model data files
+on the master node (which is the processor of rank 0 in our code)
+only and then send a copy to all the other nodes using an MPI broadcast,
+rather than using an implementation in which all the nodes would read
+the same model data files from a remotely-mounted home file system,
+which could create a bottleneck on the network in the case of a large
+number of nodes. For example, in the current call to that routine
+from \texttt{meshfem3D.f90,} we write:
+\end{quote}
+\begin{lyxcode}
+{\footnotesize !~the~variables~read~are~declared~and~stored~in~structure~CM\_V~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~if(myrank~==~0)~call~read\_crustal\_model(CM\_V)~}{\footnotesize \par}
+
+{\footnotesize !~broadcast~the~information~read~on~the~master~to~the~nodes~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(CM\_V\%thlr,NKEYS\_CRUST{*}NLAYERS\_CRUST,MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(CM\_V\%velocp,NKEYS\_CRUST{*}NLAYERS\_CRUST,MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(CM\_V\%velocs,NKEYS\_CRUST{*}NLAYERS\_CRUST,MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(CM\_V\%dens,NKEYS\_CRUST{*}NLAYERS\_CRUST,MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(CM\_V\%abbreviation,NCAP\_CRUST{*}NCAP\_CRUST,MPI\_CHARACTER,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(CM\_V\%code,2{*}NKEYS\_CRUST,MPI\_CHARACTER,0,MPI\_COMM\_WORLD,ier)~}{\footnotesize \par}
+\end{lyxcode}
+
+\section{{\normalsize \label{sec:Changing-the-Mantle}}Changing the Mantle
+Model}
+
+This section discusses how to change isotropic and anisotropic 3D
+mantle models. Usually such changes go hand-in-hand with changing
+the 3D crustal model.
+
+
+\subsection{{\normalsize \label{sub:Isotropic-Models}Isotropic Models}}
+
+The 3D mantle model S20RTS \citep{RiVaWo99} is superimposed onto
+the mantle mesh by the subroutine \texttt{mantle\_model.f90}. The
+call to this subroutine is of the form
+
+\begin{lyxcode}
+call~mantle\_model(radius,theta,phi,dvs,dvp,drho,D3MM\_V)~
+\end{lyxcode}
+Input to this routine consists of:
+
+\begin{description}
+\item [{\texttt{radius}}] Non-dimensionalized radius ($\texttt{RCMB/R\_ EARTH}<\texttt{r}<\texttt{RMOHO/R\_ EARTH}$;
+for a given 1D reference model, the constants \texttt{RCMB} and \texttt{RMOHO}
+are set in the \texttt{\small read\_compute\_parameters}\texttt{.f90}
+file). The code expects the isotropic mantle model to be defined between
+the Moho (with radius \texttt{RMOHO} in m) and the core-mantle boundary
+(CMB; radius \texttt{RCMB} in m) of a 1D reference model. When a 3D
+crustal model is superimposed, as will usually be the case, the 3D
+mantle model is stretched to fill any potential gap between the radius
+of the Moho in the 1D reference model and the Moho in the 3D crustal
+model. Thus, when the Moho in the 3D crustal model is shallower than
+the Moho in the reference model, e.g., typically below the oceans,
+the mantle model is extended to fill this gap.
+\item [{\texttt{theta}}] Colatitude in radians.
+\item [{\texttt{phi}}] Longitude in radians.
+\end{description}
+Output from the routine are the following non-dimensional perturbations:
+
+\begin{description}
+\item [{\texttt{dvs}}] Relative shear-wave speed perturbations $\delta\beta/\beta$
+at location (\texttt{radius},\texttt{theta},\texttt{phi}).
+\item [{\texttt{dvp}}] Relative compressional-wave speed perturbations
+$\delta\alpha/\alpha$.
+\item [{\texttt{drho}}] Relative density perturbations $\delta\rho/\rho$.
+\item [{\texttt{D3MM\_V}}] Fortran structure that contains the parameters,
+variables and arrays that describe the model.
+\end{description}
+You can replace the \texttt{mantle\_model.f90} file with your own
+version \textit{provided you do not change the call structure of the
+routine}, i.e., the new routine should take exactly the same input
+and produce the required relative output.
+
+Part of the file \texttt{mantle\_model.f90} is the subroutine \texttt{read\_mantle\_model}.
+The call to this routine takes argument\texttt{ D3MM\_V} and is used
+to once-and-for-all read in the databases related to S20RTS. If you
+replace the file \texttt{mantle\_model.f90} with your own implementation,
+you \textit{must} provide a \texttt{read\_mantle\_model} routine,
+even if it does nothing. Model constants and variables read by the
+routine \texttt{read\_mantle\_model} are passed to the subroutine
+\texttt{read\_mantle\_model} through the structure \texttt{D3MM\_V.}
+An alternative mantle model should use the same construct.
+
+\begin{quote}
+\textbf{NOTE:} If you decide to create your own version of file \texttt{mantle\_model.f90},
+you must add calls to \texttt{MPI\_BCAST} in file \texttt{meshfem3D.f90}
+after the call to the \texttt{read\_mantle\_model} subroutine that
+reads the isotropic mantle model once and for all in the mesher. This
+is done in order to read the (potentially large) model data files
+on the master node (which is the processor of rank 0 in our code)
+only and then send a copy to all the other nodes using an MPI broadcast,
+rather than using an implementation in which all the nodes would read
+the same model data files from a remotely-mounted home file system,
+which could create a bottleneck on the network in the case of a large
+number of nodes. For example, in the current call to that routine
+from \texttt{meshfem3D.f90,} we write:
+\end{quote}
+\begin{lyxcode}
+{\footnotesize !~the~variables~read~are~declared~and~stored~in~structure~D3MM\_V}{\footnotesize \par}
+
+{\footnotesize{}~~if(myrank~==~0)~call~read\_mantle\_model(D3MM\_V)~}{\footnotesize \par}
+
+{\footnotesize !~broadcast~the~information~read~on~the~master~to~the~nodes~~~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%dvs\_a,(NK+1){*}(NS+1){*}(NS+1),MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%dvs\_b,(NK+1){*}(NS+1){*}(NS+1),MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%dvp\_a,(NK+1){*}(NS+1){*}(NS+1),MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%dvp\_b,(NK+1){*}(NS+1){*}(NS+1),MPI\_DOUBLE\_PRECISION,}{\footnotesize \par}
+
+{\footnotesize{}~~~~~~~~~~0,MPI\_COMM\_WORLD,ier)~~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%spknt,NK+1,MPI\_DOUBLE\_PRECISION,0,MPI\_COMM\_WORLD,ier)~~~~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%qq0,(NK+1){*}(NK+1),MPI\_DOUBLE\_PRECISION,0,MPI\_COMM\_WORLD,ier)~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(D3MM\_V\%qq,3{*}(NK+1){*}(NK+1),MPI\_DOUBLE\_PRECISION,0,MPI\_COMM\_WORLD,ier)~}{\footnotesize \par}
+\end{lyxcode}
+
+\subsection{{\normalsize \label{sub:Anisotropic-Models}Anisotropic Models}}
+
+Three-dimensional anisotropic mantle models may be superimposed on
+the mesh based upon the subroutine
+
+\begin{lyxcode}
+anisotropic\_mantle\_model.f90
+\end{lyxcode}
+The call to this subroutine is of the form
+
+\begin{lyxcode}
+call~anisomantlemodel(r,theta,phi,rho,~\&~
+
+~~~~c11,c12,c13,c14,c15,c16,c22,c23,c24,c25,c26,~\&~
+
+~~~~c33,c34,c35,c36,c44,c45,c46,c55,c56,c66,AMM\_V)~
+\end{lyxcode}
+Input to this routine consists of:
+
+\begin{description}
+\item [{\texttt{r}}] Non-dimensionalized radius ($\texttt{RCMB/R\_ EARTH}<\texttt{r}<\texttt{RMOHO/R\_ EARTH}$;
+for a given 1D reference model, the constants \texttt{RCMB} and \texttt{RMOHO}
+are set in the \texttt{\small read\_compute\_parameters}\texttt{.f90}
+file). The code expects the anisotropic mantle model to be defined
+between the Moho and the core-mantle boundary (CMB). When a 3D crustal
+model is superimposed, as will usually be the case, the 3D mantle
+model is stretched to fill any potential gap between the radius of
+the Moho in the 1D reference model and the Moho in the 3D crustal
+model. Thus, when the Moho in the 3D crustal model is shallower than
+the Moho in the reference model, e.g., typically below the oceans,
+the mantle model is extended to fill this gap.
+\item [{\texttt{theta}}] Colatitude in radians.
+\item [{\texttt{phi}}] Longitude in radians.
+\end{description}
+Output from the routine consists of the following non-dimensional
+model parameters:
+
+\begin{description}
+\item [{\texttt{rho}}] Non-dimensionalized density $\rho$.
+\item [{\texttt{c11},}] \textbf{$\cdots$,} \texttt{\textbf{c66}} 21 non-dimensionalized
+anisotropic elastic parameters.
+\item [{\texttt{AMM\_V}}] Fortran structure that contains the parameters,
+variables and arrays that describe the model.
+\end{description}
+You can replace the \texttt{anisotropic\_mantle\_model.f90} file by
+your own version \textit{provided you do not change the call structure
+of the routine}, i.e., the new routine should take exactly the same
+input and produce the required relative output. Part of the file \texttt{anisotropic\_mantle\_model.f90}
+is the subroutine \texttt{read\_aniso\_mantle\_model}. The call to
+this routine takes argument \texttt{AMM\_V} and is used to once-and-for-all
+read in the static databases related to the anisotropic model. When
+you choose to replace the file \texttt{anisotropic\_mantle\_model.f90}
+with your own implementation you \textit{must} provide a \texttt{read\_aniso\_mantle\_model}
+routine, even if it does nothing. Model constants and variables read
+by the routine \texttt{read\_mantle\_model} are passed through the
+structure \texttt{AMM\_V}. An alternative anisotropic mantle model
+should use the same construct.
+
+\begin{quote}
+\textbf{NOTE:} If you decide to create your own version of file \texttt{anisotropic\_mantle\_model.f90},
+you must add calls to \texttt{MPI\_BCAST} in file \texttt{meshfem3D.f90}
+after the call to the \texttt{read\_aniso\_mantle\_model} subroutine
+that reads the anisotropic mantle model once and for all in the mesher.
+This is done in order to read the (potentially large) model data files
+on the master node (which is the processor of rank 0 in our code)
+only and then send a copy to all the other nodes using an MPI broadcast,
+rather than using an implementation in which all the nodes would read
+the same model data files from a remotely-mounted home file system,
+which could create a bottleneck on the network in the case of a large
+number of nodes. For example, in the current call to that routine
+from \texttt{meshfem3D.f90,} we write:
+\end{quote}
+\begin{lyxcode}
+{\footnotesize !~the~variables~read~are~declared~and~stored~in~structure~AMM\_V}{\footnotesize \par}
+
+{\footnotesize{}~~if(myrank~==~0)~call~read\_aniso\_mantle\_model(AMM\_V)}{\footnotesize \par}
+
+{\footnotesize !~broadcast~the~information~read~on~the~master~to~the~nodes}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(AMM\_V\%npar1,1,MPI\_INTEGER,0,MPI\_COMM\_WORLD,ier)~~~~}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(AMM\_V\%beta,14{*}34{*}37{*}73,MPI\_DOUBLE\_PRECISION,0,MPI\_COMM\_WORLD,ier)}{\footnotesize \par}
+
+{\footnotesize{}~~call~MPI\_BCAST(AMM\_V\%pro,47,MPI\_DOUBLE\_PRECISION,0,MPI\_COMM\_WORLD,ier)}{\footnotesize \par}
+\end{lyxcode}
+Rotation of the anisotropic tensor elements from one coordinate system
+to another coordinate system may be accomplished based upon the subroutine
+\texttt{rotate\_aniso\_tensor}. Use of this routine requires understanding
+the coordinate system used in \texttt{SPECFEM3D\_GLOBE}, as discussed
+in Appendix~\ref{cha:Reference-Frame-Convention}.
+
+
+\section{{\normalsize \label{sec:Anelastic-Models}}Anelastic Models}
+
+Three-dimensional anelastic (attenuation) models may be superimposed
+onto the mesh based upon your subroutine \texttt{\{attenuation\_model}\}.
+The call to this routine is as follows
+
+\begin{lyxcode}
+call~attenuation\_model(radius,~latitude,~longitude,~Qmu,~idoubling)
+\end{lyxcode}
+Input to this routine consists of:
+
+\begin{description}
+\item [{\texttt{radius}}] scaled radius of the earth: $0\,(\mathrm{center})<=r\,<=1$(surface)
+\item [{\texttt{latitude}}] Latitude in degrees: $-90^{\circ}<=\theta<=90^{\circ}$
+\item [{\texttt{longitude}}] Longitude in degrees: $-180^{\circ}<=\phi<=180^{\circ}$
+\end{description}
+Output to this routine consists of:
+
+\begin{description}
+\item [{\texttt{Qmu}}] Shear wave quality factor: $0<Q_{\mu}<5000$
+\end{description}
+If run without modification, a PREM attenuation structure will be
+implemented, using the routine \texttt{\small \{attenuation\_model}~\\
+\texttt{\small \_1D\_PREM\}}, found in \texttt{\small attenuation\_model.f90},
+within the \texttt{\small \{get\_model\}} routine.
+
+To create your own attenuation model, you need to modify your model
+using the \texttt{\small \{attenuation\_model\_1D\_PREM\}} subroutine
+and the example routine above as a guide. Replace the call to \texttt{\small \{attenuation\_model\_1D\_PREM\}}
+in \texttt{\small \{get\_model\}} to your own subroutine.
+
+Note that the resolution and maximum value of anelastic models are
+truncated. This speeds the construction of the standard linear solids
+during the meshing stage. To change the resolution, currently at one
+significant figure following the decimal, or the maximum value (5000),
+consult \texttt{constants.h}. In order to prevent unexpected results,
+quality factors $Q_{\mu}$ should never be equal to 0 outside of the
+inner core.
+
+
+\chapter{Post-Processing Scripts}
+
+Several post-processing scripts/programs are provided in the \texttt{UTILS/seis\_process}
+directory, and most of them need to be adjusted when used on different
+systems, for example, the path of the executable programs. Here we
+only list the available scripts and provide a brief description, and
+you can either refer to the related sections for detailed usage or,
+in a lot of cases, type the script/program name without arguments
+for its usage.
+
+
+\section{Clean Local Database}
+
+After all the simulations are done, you may need to clean the local
+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/}:
+
+\begin{lyxcode}
+cleanbase.pl~machines
+\end{lyxcode}
+
+\section{Process Data and Synthetics\label{sec:Process-data-and-syn}}
+
+In many cases, the SEM synthetics are calculated and compared to data
+seismograms recorded at seismic stations. Since the SEM synthetics
+are accurate for a certain frequency range, both the original data
+and the synthetics need to be processed before a comparison can be
+made. We generally use the following scripts:
+
+
+\subsection{\texttt{process\_data.pl}}
+
+This script cuts a given portion of the original data, filters it,
+transfers the data into a displacement record, and picks the first
+P and S arrivals. For more functionality, type `\texttt{process\_data.pl}'
+without any argument. An example of the usage of the script:
+
+\begin{lyxcode}
+{\small process\_data.pl~-m~CMTSOLUTION~-l~0/4000~-t~40/500~-i~-p~-x~bp~1999.330{*}.LH?.SAC}{\small \par}
+\end{lyxcode}
+which has cut all the sac files between 0 and 4000 seconds, filtered
+them between 40 and 500 seconds, transfered them into displacement
+records, picked the first P and S arrivals, and add suffix `\texttt{bp}'
+to the file names.
+
+Note that all of the scripts in this section actually use the SAC,
+saclst and/or IASP91 to do the core operations; therefore make sure
+that SAC, saclst and IASP91 packages are installed properly on your
+system, and that all the environment variables are set properly before
+running these scripts.
+
+
+\subsection{\texttt{\label{sub:process_syn.pl}process\_syn.pl}}
+
+This script converts the synthetic output from the SEM code from ASCII
+to SAC format, and performs similar operations as `\texttt{process\_data.pl}'.
+An example of the usage of the script:
+
+\begin{lyxcode}
+{\footnotesize process\_syn.pl~-m~CMTSOLUTION~-h~-a~STATIONS~-l~0/4000~-t~40/500~-p~-x~bp~syn/{*}.LH?.semd}{\footnotesize \par}
+\end{lyxcode}
+which will convolve the synthetics with a triangular source-time function
+from the \texttt{CMTSOLUTION} file, convert the synthetics into SAC
+format, add event and station information into the SAC headers, cut
+the SAC files between 0 and 4000 seconds, filter them between 40 and
+500 seconds, pick the first P and S arrivals, and add the suffix `\texttt{bp}'
+to the file names.
+
+More options are available for this script, such as adding time shift
+to the origin time of the synthetics, convolving the synthetics with
+a triangular source time function with a given half duration, etc.
+Type \texttt{process\_syn.pl} without any argument for a detailed
+usage.
+
+
+\subsection{\texttt{rotate.pl}}
+
+To rotate the horizontal components of both the data and the synthetics
+(LHN and LHE) to the transverse and radial direction (LHT and LHR),\texttt{\small{}
+}use{\small{} }\texttt{\small rotate.pl}:
+
+\begin{lyxcode}
+rotate.pl~-l~0~-L~4000~-d~DATA/{*}.LHE.SAC.bp~
+
+rotate.pl~-l~0~-L~4000~SEM/{*}.LHE.semd.sac.bp~
+\end{lyxcode}
+where the first command performs rotation on the SAC data obtained
+through IRIS (which may have timing information written in the filename),
+while the second command rotates the processed synthetics.
+
+For synthetics, another (simpler) option is to set flag \texttt{ROTATE\_SEISMOGRAMS\_RT}
+to \texttt{.true.} in the parameter file \texttt{DATA/Par\_file}.
+
+
+\subsection{\texttt{clean\_sac\_headers\_after\_crash.sh}}
+
+Note: You need to have the \texttt{sismoutil-0.9b} package installed
+on your computer if you want to run this script on binary SAC files.
+The software is available at the ORFEUS web site \url{www.orfeus-eu.org}.
+
+In case the simulation crashes during run-time without computing and
+writing all time steps, the SAC files (if flags \texttt{OUTPUT\_SEISMOS\_SAC\_ALPHANUM}
+or \texttt{OUTPUT\_SEISMOS\_SAC\_BINARY} have been set to \texttt{.true.})
+are corrupt and cannot be used properly in SAC. If the simulation
+ran long enough so that the synthetic data may still be of use, you
+can run the script called \texttt{clean\_sac\_headers\_after\_crash.sh}
+(located in the \texttt{UTILS} directory) on the SAC files to correct
+the header variable NPTS to the actually written number of time steps.
+The script must be called from the \texttt{SPECFEM3D} main directory,
+and the input argument to this script is simply a list of SAC seismogram
+files.
+
+
+\section{Map Local Database}
+
+A sample program \texttt{remap\_database} is provided to map the local
+database from a set of machines to another set of machines. This is
+especially useful when you want to run mesher and solver, or different
+types of solvers separately through a scheduler (refer to Chapter~\ref{cha:Running-Scheduler}).
+
+\begin{lyxcode}
+run\_lsf.bash~-{}-gm-no-shmem~-{}-gm-copy-env~remap\_database
+
+old\_machines~150~{[}old\_jobid~new\_jobid]
+\end{lyxcode}
+where \texttt{old\_machines} is the LSF machine file used in the previous
+simulation, and \texttt{150} is the number of processors in total.
+Note that you need to supply \texttt{old\_jobid} and \texttt{new\_jobid(\%J)}
+which are the LSF job-IDs for the old and new run if your databases
+are stored in a sub-directory named after the jobid on the scratch
+disk.
+
+
+\chapter*{\label{cha:Bug-Reports-and}Bug Reports and Suggestions for Improvements}
+
+To report bugs or suggest improvements to the code, please send an
+e-mail to the CIG Computational Seismology Mailing List \url{cig-seismo at geodynamics.org}
+or Jeroen Tromp \url{jtromp-AT-gps.caltech.edu}, and/or use our online
+bug tracking system Roundup \url{www.geodynamics.org/roundup}.
+
+
+\chapter*{\label{cha:Notes-and-Acknowledgements}Notes and Acknowledgements}
+
+In order to keep the software package thread-safe in case a multithreaded
+implementation of MPI is used, developers should not add modules or
+common blocks to the source code but rather use regular subroutine
+arguments (which can be grouped in ``derived types'' if needed for
+clarity).
+
+The Gauss-Lobatto-Legendre subroutines in \texttt{gll\_library.f90}
+are based in part on software libraries from the Massachusetts Institute
+of Technology, Department of Mechanical Engineering (Cambridge, Massachusetts).
+The non-structured global numbering software was provided by Paul
+F. Fischer (Brown University, Providence, Rhode Island).
+
+OpenDX \url{www.opendx.org} is open-source based on IBM Data Explorer,
+AVS \url{www.avs.com} is a trademark of Advanced Visualization Systems,
+and ParaView \url{www.paraview.com} is an open-source visualization
+platform.{\small{} }{\small \par}
+
+The main developers of the \texttt{SPECFEM3D\_GLOBE} source code are
+Dimitri Komatitsch, Jeroen Tromp, Qinya Liu and David Michéa. The
+following individuals (listed in alphabetical order) have also contributed
+to the development of the source code: Min Chen, Vala Hjörleifsdóttir,
+Nicolas Le Goff, Brian Savage, Bernhard Schuberth, Anne Sieminski,
+Leif Strand and Peter van Keken. The following individuals (listed
+in alphabetical order) contributed to this manual: Min Chen, Vala
+Hjörleifsdóttir, Sue Kientz, Dimitri Komatitsch, Qinya Liu, Alessia
+Maggi, David Michéa, 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/}.
+
+Please e-mail your feedback, questions, comments, and suggestions
+to Jeroen Tromp \url{jtromp-AT-gps.caltech.edu} or to the CIG Computational Seismology Mailing List \url{cig-seismo at geodynamics.org}.
+
+
+\chapter*{\label{cha:Copyright}Copyright}
+
+Main authors: Dimitri Komatitsch and Jeroen Tromp
+
+Seismological Laboratory, California Institute of Technology, U.S.,
+and University of Pau / CNRS / INRIA, France
+
+© California Institute of Technology and University of Pau / CNRS
+/ INRIA, February 2008
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published
+by the Free Software Foundation (see Appendix \ref{cha:License}).
+
+{\small \bibliography{bibliography}
+}{\small \par}
+
+\appendix
+
+\chapter{\label{cha:Reference-Frame-Convention}Reference Frame Convention}
+
+The code uses the following convention for the Cartesian reference
+frame:
+
+\begin{itemize}
+\item the $x$ axis points East
+\item the $y$ axis points North
+\item the $z$ axis points up
+\end{itemize}
+Note that this convention is different from both the \citet{AkRi80}
+convention and the Harvard Centroid-Moment Tensor (CMT) convention.
+The Aki \& Richards convention is
+
+\begin{itemize}
+\item the $x$ axis points North
+\item the $y$ axis points East
+\item the $z$ axis points down
+\end{itemize}
+and the Harvard CMT convention is
+
+\begin{itemize}
+\item the $x$ axis points South
+\item the $y$ axis points East
+\item the $z$ axis points up
+\end{itemize}
+
+\chapter{\label{cha:Non-Dimensionalization-Conventions}Non-Dimensionalization
+Conventions{\small{} }}
+
+All physical parameters used by the code are non-dimensionalized according
+to the conventions summarized in Table~{\small \ref{table:conventions}.
+}%
+\begin{table}[ht]
+\noindent \begin{centering}
+{\small }\begin{tabular}{|c|c|}
+\hline
+quantity (units) & non-dimensionalized with \tabularnewline
+\hline
+distance (m) & \texttt{R\_EARTH} \tabularnewline
+time (s) & $\sqrt{\texttt{PI}\times\texttt{GRAV}\times\texttt{RHOAV}}$ \tabularnewline
+density (kg/m$^{3}$) & \texttt{RHOAV} \tabularnewline
+\hline
+\end{tabular}
+\par\end{centering}{\small \par}
+
+\caption{Non-dimensionalization employed by the code. The constants \texttt{R\_EARTH}
+(the radius of the Earth), \texttt{PI} (the number $\pi$), \texttt{GRAV}
+(the universal gravitational constant), and \texttt{RHOAV} (the Earth's
+average density) are defined in the \texttt{constants.h} file. }
+
+
+{\small \label{table:conventions} }
+\end{table}
+{\small \par}
+
+
+\chapter{Benchmarks}
+
+\citet{KoTr02a,KoTr02b} carefully benchmarked the spectral-element
+simulations of global seismic waves against normal-mode seismograms.
+Version 4.0 of \texttt{SPECFEM3D\_GLOBE} has been benchmarked again
+following the same procedure.
+
+In this appendix we present two tests: a `long-period' (periods longer
+than 17~s) simulation of a shallow event in isotropic PREM \citep{DzAn81}
+without the ocean layer, without attenuation but including the effects
+of self-gravitation (in the Cowling approximation) (Figures \ref{fig:Vanuatu-with-Vertical}
+and \ref{fig:Vanuatu-with-Transverse}), and a `short-period' (periods
+longer than 9~s) simulation of a deep event in transversely isotropic
+PREM without the ocean layer and including the effects of self-gravitation
+and attenuation (Figures \ref{fig:Bolivia-with-Vertical}, \ref{fig:Bolivia-with-Transverse}
+and \ref{fig:Bolivia-PKP}).
+
+%
+\begin{figure}[h]
+\noindent \begin{centering}
+\includegraphics[scale=0.75,bb = 0 0 200 100, draft, type=eps]{/Users/sue/specfem3d/globe/USER_MANUAL/figures/vanuatu_vertical.eps}\caption{\label{fig:Vanuatu-with-Vertical} Normal-mode (blue) and SEM (red)
+vertical displacements in isotropic PREM considering the effects of
+self-gravitation but not attenuation for 13 stations at increasing
+distance from the 1999 November 26th Vanuatu event located at 15~km
+depth. The SEM computation is accurate for periods longer than 17~s.
+The seismograms have been filtered between 50~s and 500~s. The station
+names are indicated on the left. }
+
+\par\end{centering}
+\end{figure}
+%
+\begin{figure}[h]
+\noindent \begin{centering}
+\includegraphics[scale=0.75,bb = 0 0 200 100, draft, type=eps]{/Users/sue/specfem3d/globe/USER_MANUAL/figures/vanuatu_trans.eps}\caption{\label{fig:Vanuatu-with-Transverse}Same as in Figure \ref{fig:Vanuatu-with-Vertical}
+for the transverse displacements.}
+
+\par\end{centering}
+\end{figure}
+%
+\begin{figure}[h]
+\noindent \begin{centering}
+\includegraphics[scale=0.75,bb = 0 0 200 100, draft, type=eps]{/Users/sue/specfem3d/globe/USER_MANUAL/figures/bolivia_vertical.eps}\caption{\label{fig:Bolivia-with-Vertical}Normal-mode (blue) and SEM (red)
+vertical displacements in transversely isotropic PREM considering
+the effects of self-gravitation and attenuation for 12 stations at
+increasing distance from the 1994 June 9th Bolivia event located at
+647~km depth. The SEM computation is accurate for periods longer
+than 9~s. The seismograms have been filtered between 10~s and 500~s.
+The station names are indicated on the left.}
+
+\par\end{centering}
+\end{figure}
+%
+\begin{figure}[h]
+\noindent \begin{centering}
+\includegraphics[scale=0.75,bb = 0 0 200 100, draft, type=eps]{/Users/sue/specfem3d/globe/USER_MANUAL/figures/bolivia_trans.eps}\caption{\label{fig:Bolivia-with-Transverse}Same as in Figure \ref{fig:Bolivia-with-Vertical}
+for the transverse displacements.}
+
+\par\end{centering}
+\end{figure}
+
+
+%
+\begin{figure}[h]
+\noindent \begin{centering}
+\includegraphics[scale=0.75,bb = 0 0 200 100, draft, type=eps]{/Users/sue/specfem3d/globe/USER_MANUAL/figures/PKPdf_all_15s500s.eps}\caption{\label{fig:Bolivia-PKP}Seismograms recorded between 130 degrees and
+230 degrees, showing in particular the good agreement for core phases
+such as PKP. This figure is similar to Figure 24 of \citet{KoTr02a}.
+The results have been filtered between 15~s and 500~s.}
+
+\par\end{centering}
+\end{figure}
+
+
+The normal-mode synthetics are calculated with the code \texttt{QmXD}
+using mode catalogs with a shortest period of 8~s generated by the
+code \texttt{OBANI}. No free-air, tilt, or gravitational potential
+corrections were applied \citep{DaTr98}. We also turned off the effect
+of the oceans in \texttt{QmXD}.
+
+The normal-mode and SEM displacement seismograms are first calculated
+for a step source-time function, i.e., setting the parameter \texttt{half}
+\texttt{duration} in the \texttt{CMTSOLUTION} file to zero for the
+SEM simulations. Both sets of seismograms are subsequently convolved
+with a triangular source-time function using the processing script
+\texttt{UTILS/seis\_}~\\
+\texttt{process/process\_syn.pl}. They are also band-pass filtered
+and the horizontal components are rotated to the radial and transverse
+directions (with the script \texttt{UTILS/seis\_process/rotate.pl}).
+
+The match between the normal-mode and SEM seismograms is quite remarkable
+for the experiment with attenuation, considering the very different
+implementations of attenuation in the two computations (e.g., frequency
+domain versus time domain, constant Q versus absorption bands).
+
+Further tests can be found in the \texttt{EXAMPLES} directory. It
+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:License}License}
+
+\textbf{GNU GENERAL PUBLIC LICENSE Version 2, June 1991. Copyright
+(C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite
+330, Boston, MA 02111-1307 USA} \\
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+
+\section*{Preamble}
+
+The licenses for most software are designed to take away your freedom
+to share and change it. By contrast, the GNU General Public License
+is intended to guarantee your freedom to share and change free software
+-- to make sure the software is free for all its users. This General
+Public License applies to most of the Free Software Foundation's software
+and to any other program whose authors commit to using it. (Some other
+Free Software Foundation software is covered by the GNU Library General
+Public License instead.) You can apply it to your programs, too.
+
+When we speak of free software, we are referring to freedom, not price.
+Our General Public Licenses are designed to make sure that you have
+the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get
+it if you want it, that you can change the software or use pieces
+of it in new free programs; and that you know you can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone
+to deny you these rights or to ask you to surrender the rights. These
+restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis
+or for a fee, you must give the recipients all the rights that you
+have. You must make sure that they, too, receive or can get the source
+code. And you must show them these terms so they know their rights.
+
+We protect your rights with two steps:
+
+\begin{enumerate}
+\item Copyright the software, and
+\item Offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+\end{enumerate}
+Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on,
+we want its recipients to know that what they have is not the original,
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+
+Finally, any free program is threatened constantly by software patents.
+We wish to avoid the danger that redistributors of a free program
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+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+
+\section*{GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION
+AND MODIFICATION }
+
+\begin{itemize}
+
+\item[0.]This License applies to any program or other work which
+contains a notice placed by the copyright holder saying it may be
+distributed under the terms of this General Public License. The ``Program''
+below refers to any such program or work, and a ``work based on the
+Program'' means either the Program or any derivative work under copyright
+law: that is to say, a work containing the Program or a portion of
+it, either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation
+in the term ``modification.'') Each licensee is addressed as ``you.''\\
+\\
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of running
+the Program is not restricted, and the output from the Program is
+covered only if its contents constitute a work based on the Program
+(independent of having been made by running the Program). Whether
+that is true depends on what the Program does.
+
+\end{itemize}
+
+\begin{enumerate}
+\item You may copy and distribute verbatim copies of the Program's source
+code as you receive it, in any medium, provided that you conspicuously
+and appropriately publish on each copy an appropriate copyright notice
+and disclaimer of warranty; keep intact all the notices that refer
+to this License and to the absence of any warranty; and give any other
+recipients of the Program a copy of this License along with the Program.
+
+
+You may charge a fee for the physical act of transferring a copy,
+and you may at your option offer warranty protection in exchange for
+a fee.
+
+\item You may modify your copy or copies of the Program or any portion of
+it, thus forming a work based on the Program, and copy and distribute
+such modifications or work under the terms of Section 1 above, provided
+that you also meet all of these conditions:
+
+\begin{enumerate}
+\item You must cause the modified files to carry prominent notices stating
+that you changed the files and the date of any change.
+\item You must cause any work that you distribute or publish, that in whole
+or in part contains or is derived from the Program or any part thereof,
+to be licensed as a whole at no charge to all third parties under
+the terms of this License.
+\item If the modified program normally reads commands interactively when
+run, you must cause it, when started running for such interactive
+use in the most ordinary way, to print or display an announcement
+including an appropriate copyright notice and a notice that there
+is no warranty (or else, saying that you provide a warranty) and that
+users may redistribute the program under these conditions, and telling
+the user how to view a copy of this License. (Exception: if the Program
+itself is interactive but does not normally print such an announcement,
+your work based on the Program is not required to print an announcement.)
+\end{enumerate}
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be
+reasonably considered independent and separate works in themselves,
+then this License, and its terms, do not apply to those sections when
+you distribute them as separate works. But when you distribute the
+same sections as part of a whole which is a work based on the Program,
+the distribution of the whole must be on the terms of this License,
+whose permissions for other licensees extend to the entire whole,
+and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is
+to exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume
+of a storage or distribution medium does not bring the other work
+under the scope of this License.
+
+\item You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections
+1 and 2 above provided that you also do one of the following:
+
+\begin{enumerate}
+\item Accompany it with the complete corresponding machine-readable source
+code, which must be distributed under the terms of Sections 1 and
+2 above on a medium customarily used for software interchange; or,
+\item Accompany it with a written offer, valid for at least three years,
+to give any third party, for a charge no more than your cost of physically
+performing source distribution, a complete machine-readable copy of
+the corresponding source code, to be distributed under the terms of
+Sections 1 and 2 above on a medium customarily used for software interchange;
+or,
+\item Accompany it with the information you received as to the offer to
+distribute corresponding source code. (This alternative is allowed
+only for noncommercial distribution and only if you received the program
+in object code or executable form with such an offer, in accord with
+Subsection b above.)
+\end{enumerate}
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to control
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+is normally distributed (in either source or binary form) with the
+major components (compiler, kernel, and so on) of the operating system
+on which the executable runs, unless that component itself accompanies
+the executable.
+
+If distribution of executable or object code is made by offering access
+to copy from a designated place, then offering equivalent access to
+copy the source code from the same place counts as distribution of
+the source code, even though third parties are not compelled to copy
+the source along with the object code.
+
+\item You may not copy, modify, sublicense, or distribute the Program except
+as expressly provided under this License. Any attempt otherwise to
+copy, modify, sublicense or distribute the Program is void, and will
+automatically terminate your rights under this License. However, parties
+who have received copies, or rights, from you under this License will
+not have their licenses terminated so long as such parties remain
+in full compliance.
+\item You are not required to accept this License, since you have not signed
+it. However, nothing else grants you permission to modify or distribute
+the Program or its derivative works. These actions are prohibited
+by law if you do not accept this License. Therefore, by modifying
+or distributing the Program (or any work based on the Program), you
+indicate your acceptance of this License to do so, and all its terms
+and conditions for copying, distributing or modifying the Program
+or works based on it.
+\item Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor
+to copy, distribute or modify the Program subject to these terms and
+conditions. You may not impose any further restrictions on the recipients'
+exercise of the rights granted herein. You are not responsible for
+enforcing compliance by third parties to this License.
+\item If, as a consequence of a court judgment or allegation of patent infringement
+or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise)
+that contradict the conditions of this License, they do not excuse
+you from the conditions of this License. If you cannot distribute
+so as to satisfy simultaneously your obligations under this License
+and any other pertinent obligations, then as a consequence you may
+not distribute the Program at all. For example, if a patent license
+would not permit royalty-free redistribution of the Program by all
+those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended
+to apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the integrity
+of the free software distribution system, which is implemented by
+public license practices. Many people have made generous contributions
+to the wide range of software distributed through that system in reliance
+on consistent application of that system; it is up to the author/donor
+to decide if he or she is willing to distribute software through any
+other system and a licensee cannot impose that choice.
+
+This section is intended to make thoroughly clear what is believed
+to be a consequence of the rest of this License.
+
+\item If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
+copyright holder who places the Program under this License may add
+an explicit geographical distribution limitation excluding those countries,
+so that distribution is permitted only in or among countries not thus
+excluded. In such case, this License incorporates the limitation as
+if written in the body of this License.
+\item The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in
+detail to address new problems or concerns.
+
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and
+``any later version,'' you have the option of following the terms
+and conditions either of that version or of any later version published
+by the Free Software Foundation. If the Program does not specify a
+version number of this License, you may choose any version ever published
+by the Free Software Foundation.
+
+\item If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to
+ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software
+and of promoting the sharing and reuse of software generally.
+\end{enumerate}
+
+\subsection*{NO WARRANTY }
+
+\begin{itemize}
+
+\item[11.]BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS
+NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE
+LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS
+AND/OR OTHER PARTIES PROVIDE THE PROGRAM ``AS IS'' WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED
+TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
+PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+\item[12.]IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED
+TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY
+MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE
+TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED
+INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE
+OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+\end{itemize}
+
+
+\section*{END OF TERMS AND CONDITIONS }
+
+
+\subsection*{How to Apply These Terms to Your New Programs}
+
+If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make
+it free software which everyone can redistribute and change under
+these terms.
+
+To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the ``copyright'' line and a pointer to where the full notice is found.
+For example:
+
+\begin{quote}
+One line to give the program's name and a brief idea of what it does.
+Copyright {\footnotesize © (}year) (name of author)
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published
+by the Free Software Foundation; either version 2 of the License,
+or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software Foundation,
+Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+\end{quote}
+Also add information on how to contact you by electronic and paper
+mail.
+
+If the program is interactive, make it output a short notice like
+this when it starts in an interactive mode:
+
+\begin{quote}
+Gnomovision version 69, Copyright © year name of author Gnomovision
+comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This
+is free software, and you are welcome to redistribute it under certain
+conditions; type `show c' for details.
+\end{quote}
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use
+may be called something other than `show w' and `show c'; they could
+even be mouse-clicks or menu items -- whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or
+your school, if any, to sign a ``copyright disclaimer'' for the program,
+if necessary. Here is a sample; alter the names:
+
+\begin{quote}
+Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+`Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+(signature of Ty Coon)\\
+1 April 1989 \\
+Ty Coon, President of Vice
+\end{quote}
+This General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library,
+you may consider it more useful to permit linking proprietary applications
+with the library. If this is what you want to do, use the GNU Library
+General Public License instead of this License.
+\end{document}
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