[cig-commits] [commit] master, python-removal, rajesh-petsc-schur: Removed Cookbook 10 from the CitcomS manual (6ceb31d)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Nov 5 19:01:50 PST 2014
Repository : https://github.com/geodynamics/citcoms
On branches: master,python-removal,rajesh-petsc-schur
Link : https://github.com/geodynamics/citcoms/compare/464e1b32299b15819f93efd98d969cddb84dfe51...f97ae655a50bdbd6dac1923a3471ee4dae178fbd
>---------------------------------------------------------------
commit 6ceb31dba5be3b9eeeebe7711090bef10c5dc717
Author: Rajesh Kommu <rajesh.kommu at gmail.com>
Date: Wed Jun 25 14:58:24 2014 -0700
Removed Cookbook 10 from the CitcomS manual
>---------------------------------------------------------------
6ceb31dba5be3b9eeeebe7711090bef10c5dc717
doc/citcoms-manual.pdf | Bin 12581683 -> 11886680 bytes
doc/citcoms-manual.tex | 402 +------------------------------------------------
2 files changed, 2 insertions(+), 400 deletions(-)
diff --git a/doc/citcoms-manual.pdf b/doc/citcoms-manual.pdf
index b53351e..3cae9c3 100644
Binary files a/doc/citcoms-manual.pdf and b/doc/citcoms-manual.pdf differ
diff --git a/doc/citcoms-manual.tex b/doc/citcoms-manual.tex
index 9639904..6fdd07e 100644
--- a/doc/citcoms-manual.tex
+++ b/doc/citcoms-manual.tex
@@ -2292,8 +2292,7 @@ Users familiar with GMT are welcome to contribute a fix to the script.}
\section{Introduction}
These cookbook examples are meant to serve as a guide to some of the
-types of problems CitcomS can solve. Each of these cookbook problems
-will only run with CitcomS if Pyre is enabled. Cookbook examples range
+types of problems CitcomS can solve. Cookbook examples range
from regional to full spherical shell problems that address traditional
mantle convection problems. These cookbook examples are distributed
with the package under the \texttt{examples} directory. However, you
@@ -2309,11 +2308,7 @@ formulation for studying short wavelength dynamics topography. Cookbook
7 introduces thermo-chemical convection problem and tuning of the
Conjugate Gradient velocity solver. Cookbook 8 introduces compressible
convection problem, checkpointing/restarting, geoid and tuning of
-the Multigrid and Uzawa velocity solver. Cookbook 9 introduces embedding
-one CitcomS domain within another CitcomS domain, and further tuning
-of the advection solver. Cookbook 10 introduces how to convert the
-convection field to seismic velocities and how to generate synthetic
-seismograms using SPECFEM3D\_GLOBE at the CIG Seismology Web Portal.\newpage{}
+the Multigrid and Uzawa velocity solver.
\section{\label{sec:Cookbook-1:-Global}Cookbook 1: Global Model}
@@ -4053,399 +4048,6 @@ direction. The temperature isosurface is at 0.8. The grid spacings
of both meshes are reduced approximately threefold for better visualization.}
\end{figure}
-
-\newpage{}
-
-
-\section{Cookbook 10: Synthetic Seismograms from Mantle Convection Models}
-
-
-\subsection{Problem}
-
-This example is a step-up of Cookbook \ref{fig:Cookbook-7:-The},
-thermo-chemical convection within a full spherical shell domain. Composition
-heterogeneity exists in the Earth mantle. The density anomalies due
-to the composition heterogeneity, as well as due to the thermal heterogeneity,
-drive the convection flow. The same composition heterogeneity causes
-seismic velocity anomalies. The goal is to convert the mantle convection
-models, with the aid of a mineral physics model, to seismic anomalies,
-and then generate synthetic seismograms using SPECFEM3D\_GLOBE.
-
-
-\subsection{Solution}
-
-This cookbook uses CitcomS and SPECFEM3D\_GLOBE. SPECFEM3D\_GLOBE
-is a spectral element code to simulate seismic wave propogation in
-the global scale. To use SPECFEM3D\_GLOBE, you can either download
-the code from this link \url{geodynamics.org/cig/software/packages/seismo/specfem3d-globe/}
-and install it on your machine, which requires a Fortran 90 compiler
-and a cluster, or you can go to CIG Seismology Web Portal \url{https://crust.geodynamics.org/portals/seismo/}
-to launch a job, which only requires a browser. We will use the later
-approach in the cookbook.
-
-
-\subsubsection{Running CitcomS}
-
-Most of the parameters are copied from Cookbook \ref{fig:Cookbook-7:-The}.
-We will highlight a few differences. We use a higher Rayleigh number.
-\begin{lyxcode}
-rayleigh~=~1e9
-\end{lyxcode}
-The radius of the bottom surface is set to 0.546 in the cookbook,
-which must be smaller than the CMB radius in SPECFEM3D\_GLOBE. (If
-PREM is used as the 1D reference model in SPECFEM3D\_GLOBE, the CMB
-radius is 0.5462.)
-\begin{lyxcode}
-radius\_inner~=~0.546~
-\end{lyxcode}
-We convert the temperature and composition fields to seismic velocities
-using a mineral phyiscs model. Currently, there is only one model
-implemented, based on the model of \textit{Trampert, Vacher, and Vlaar}\cite{Trampert mineral physics model 2001}.
-In their paper, the (depth dependent) temperature and composition
-derivatives of seismic velocities are given as polynomial coefficients.
-Note that the paper has its own reference profile, and is only valid
-between 1000 km < depth < 2600 km. We will extend the model to whole
-mantle and use PREM as the reference profile. This clearly is over-stretching
-the model, but we are using it for demonstration purposes.
-\begin{lyxcode}
-mineral\_physics\_model~=~3
-\end{lyxcode}
-We will output the converted density and seismic velocities for SPECFEM3D\_GLOBE
-consumption. This option enables the binary seismic output (\texttt{{*}.seismic.{*}}
-files), as well as other binary output (\texttt{{*}.domain} and \texttt{{*}.coord\_bin.{*}}
-files) that SPECFEM3D\_GLOBE will read. The formats of these binary
-files are provided in Appendix \ref{sec:Misc.-Binary-Output}.
-\begin{lyxcode}
-output\_optional~=~tracer,~comp\_nd,~seismic
-\end{lyxcode}
-
-\subsubsection{Example: Synthetic Seismograms from Mantle Convection Model, cookbook10.cfg}
-\begin{lyxcode}
-\#~Cookbook~10:~Synthetic~Seismograms~from~Mantle~Convection~Models
-
-{[}CitcomS{]}
-
-solver~=~full
-
-steps~=~15~\\
-~\\
-{[}CitcomS.controller{]}
-
-monitoringFrequency~=~5~\\
-~\\
-{[}CitcomS.solver{]}
-
-datadir~=~output
-
-datafile~=~cookbook10
-
-rayleigh~=~1e9~\\
-~\\
-{[}CitcomS.solver.mesher{]}
-
-radius\_inner~=~0.546~\\
-~\\
-{[}CitcomS.solver.ic{]}
-
-num\_perturbations~=~1
-
-perturbl~=~3
-
-perturbm~=~2
-
-perturblayer~=~5
-
-perturbmag~=~0.05~\\
-~\\
-{[}CitcomS.solver.output{]}
-
-output\_optional~=~tracer,comp\_nd,seismic~\\
-~\\
-{[}CitcomS.solver.param{]}
-
-mineral\_physics\_model~=~3~\\
-~\\
-{[}CitcomS.solver.tracer{]}
-
-tracer~=~on
-
-tracer\_ic\_method~=~0
-
-tracers\_per\_element~=~20
-
-tracer\_file~=~tracer.dat~\\
-~\\
-tracer\_flavors~=~2
-
-ic\_method\_for\_flavors~=~0
-
-z\_interface~=~0.7~\\
-~\\
-chemical\_buoyancy~=~1
-
-buoy\_type~=~1
-
-buoyancy\_ratio~=~0.5~\\
-~\\
-regular\_grid\_deltheta~=~1.0
-
-regular\_grid\_delphi~=~1.0~\\
-~\\
-{[}CitcomS.solver.vsolver{]}
-
-Solver~=~cgrad
-
-accuracy~=~1e-04
-
-vlowstep~=~1000
-
-piterations~=~1000~\\
-~\\
-\#~Assign~the~viscosities.
-
-{[}CitcomS.solver.visc{]}
-
-VISC\_UPDATE~=~on
-
-num\_mat~=~4
-
-visc0~=~1,1,1,1
-
-TDEPV~=~on
-
-rheol~=~4
-
-viscE~=~0.2,0.2,0.2,0.2
-
-viscT~=~0,0,0,0
-
-viscZ~=~0,0,0,0
-
-VMIN~=~on
-
-visc\_min~=~1.0
-
-VMAX~=~on
-
-visc\_max~=~100.0
-\end{lyxcode}
-
-\subsubsection{Running SPECFEM3D\_GLOBE from CIG Seismology Web Portal}
-
-Using your favorite browser, go to the CIG Seismology Web Portal \url{https://crust.geodynamics.org/portals/seismo/}.
-Free registration is required to use the portal. Your initial account
-has 10,000 SUs (CPU-hours) allocated. A short (20 minutes of seismograms),
-low-resolution SPECFEM3D\_GLOBE run consumes about 450 SUs. A short,
-high-resolution SPECFEM3D\_GLOBE run consumes about 1,000 SUs. Further
-SUs can be allocated upon request.
-
-After you login to the portal, take a few minutes to read the instructions
-and familiarize yourself with the interface. You will see a toolbar
-with big icons on the top and several grayed-out tabs below the toolbar.
-The toolbar allows you to specify the earthquake source (\texttt{Events}),
-the receivers (\texttt{Stations}), and simulation parameters (\texttt{3D
-Parameters}), including the resolution (\texttt{Mesh}) and the seismic
-velocity model for the crust and mantle (\texttt{3D Models}). In the
-cookbook, we will upload the result of CitcomS as a 3D Model and upload
-our own fictitious stations and event.
-
-\begin{center}
-\includegraphics[scale=0.6]{graphics/portal-upload-a.png}
-\par\end{center}
-
-Click on the \texttt{3D Models} icon (1), and the \texttt{Upload}
-tab (2), then click on the link \texttt{citcoms\_isotropic\_no\_crust.tgz}
-(3) to download the tar file to your machine. The tar file you just
-downloaded contains the code that reads CitcomS output and feeds the
-seismic velocities to SPECFEM3D\_GLOBE. However, the tarball does
-not contains the actual CitcomS output, which will be provided by
-you later. As you might have guessed from the filename, the code will
-generate an isotropic mantle without an overlay of a 3D crust, such
-as the CRUST2.0 model. The 3D crust model obeys the continent-ocean
-distribution of current Earth. Since our CitcomS model has no notation
-on where is the Pacific and where is Asia, we do not want to impose
-a 3D crust model. You can untar the file by running:
-\begin{lyxcode}
-\$~gunzip~-c~citcoms\_isotropic\_no\_crust.tgz~|~tar~xf~-
-\end{lyxcode}
-You will supply the CitcomS output to the code. Copy these CitcomS
-output files \texttt{cookbook.domain}, \texttt{cookbook.coord\_bin.{*}},
-and \texttt{cookbook.seismic.{*}.15} to the directory \texttt{citcoms\_isotropic\_no\_crust/shared/},
-so that the content of the directory looks like:
-\begin{lyxcode}
-\$~ls~citcoms\_isotropic\_no\_crust/shared/
-
-cookbook10.coord\_bin.0~~~cookbook10.seismic.0.15~
-
-cookbook10.coord\_bin.1~~~cookbook10.seismic.10.15~
-
-cookbook10.coord\_bin.10~~cookbook10.seismic.11.15~
-
-cookbook10.coord\_bin.11~~cookbook10.seismic.1.15~
-
-cookbook10.coord\_bin.2~~~cookbook10.seismic.2.15~
-
-cookbook10.coord\_bin.3~~~cookbook10.seismic.3.15~
-
-cookbook10.coord\_bin.4~~~cookbook10.seismic.4.15~
-
-cookbook10.coord\_bin.5~~~cookbook10.seismic.5.15~
-
-cookbook10.coord\_bin.6~~~cookbook10.seismic.6.15~
-
-cookbook10.coord\_bin.7~~~cookbook10.seismic.7.15~
-
-cookbook10.coord\_bin.8~~~cookbook10.seismic.8.15~
-
-cookbook10.coord\_bin.9~~~cookbook10.seismic.9.15~
-
-cookbook10.domain
-\end{lyxcode}
-These files contain the coordinate, density, and seismic velocities
-data. We will need to tell SPECFEM3D\_GLOBE where to find the CitcomS
-output. Edit the header file \texttt{citcoms\_isotropic\_no\_crust/citcoms\_parm.h}
-to become:
-\begin{lyxcode}
-/{*}~filename~prefix~of~citcoms~output~{*}/
-
-const~char~citcoms\_model\_filename\_base{[}{]}~=~\textquotedbl{}@THIS\_DIR@/shared/cookbook10\textquotedbl{};
-
-
-
-/{*}~time~step~of~citcoms~output~{*}/
-
-const~int~citcoms\_step~=~15;
-\end{lyxcode}
-The portal has a few conventions on where to put the data. First,
-the magic string \texttt{@THIS\_DIR@} will be replaced by the absolute
-path when the tar file is expanded by the portal. Second, the tar
-file will be distributed to all computer nodes when portal launches
-the job. Third, the subdirectory \texttt{shared/} is special such
-that files in this directory will not be distributed to all computer
-nodes. Data files of huge size should be put in this directory. You
-might want to edit \texttt{citcoms\_isotropic\_no\_crust/description.txt}
-to provide a description of your model. The text in this file will
-be displayed on the portal. The final step before uploading is to
-create a new tar file containing the code and data.
-\begin{lyxcode}
-\$~tar~cf~cookbook10.tar~citcoms\_isotropic\_no\_crust/
-
-\$~gzip~cookbook10.tar
-\end{lyxcode}
-Now, you can upload the data by clicking on the \texttt{Browse} button
-(4), choosing \texttt{cookbook10.tar.gz} from the resulting dialog
-box, then clicking on the \texttt{Upload} button. After the portal
-confirms that the upload is successful, click on the \texttt{3D Models}
-icon again; you will see \texttt{cookbook10} is among the available
-3D models.
-
-\begin{center}
-\includegraphics[scale=0.6]{graphics/portal-param-a.png}
-\par\end{center}
-
-You have to select a few parameters for a SPECFEM3D\_GLOBE run. Click
-on the \texttt{3D Parameters} icon (5), the \texttt{New} tab (6),
-select the parameters as shown in the figure above, and save the parameters
-for later use. We will use a global mesh that is capable of resolving
-seismic waves of 27 second period. Since CitcomS mesh is a perfect
-sphere, you need to disable \texttt{topography} and \texttt{ellipticity}
-to have a matching mesh in SPECFEM3D\_GLOBE. The \texttt{oceans} is
-disabled because we don't have a 3D crust.
-
-We will provide our own fictitious earthquake source and seismic stations.
-The earthquake source is defined in \texttt{cmt-solution.cookbook10}
-in the cookbook directory. The source is located at 15 km depth of
-$0^{\circ}$N, $0^{\circ}$E. The half duration of the source is 0
-second, which means a step function is used. Click on the \texttt{Events}
-icon and the \texttt{upload} tab to upload the file \texttt{cmt-solution.cookbook10}.
-The stations are defined in \texttt{stations.cookbook10} in the cookbook
-directory. The stations are on the Equator and are 70 to 100 degrees
-away from the source. Click on the \texttt{Stations} icon and the
-\texttt{upload} tab to upload the file \texttt{stations.cookbook10}.
-
-\begin{center}
-\includegraphics[scale=0.75]{graphics/portal-run-a.png}
-\par\end{center}
-
-Finally, we are ready to launch a SPECFEM3D\_GLOBE simulation. Click
-on the \texttt{Runs} icon (7), then the \texttt{New} tab (8), and
-select our recently uploaded event, stations and parameters. Set the
-record length to 30 minutes, which will give us synthetic seismograms
-of 30 minutes. Click the \texttt{Save} button to save the settings.
-
-\begin{center}
-\includegraphics[scale=0.6]{graphics/portal-submit2-a.png}
-\par\end{center}
-
-You will be presented with a summary of the simulation settings, including
-a map showing the location of the events and stations. After you have
-reviewed all settings, scroll to the bottom of the page. Click on
-the \texttt{Start} button. The request for the simulation is sent
-to the TeraGrid supercomputing center. Your simulation will be waiting
-in the queue and will be launched within several hours. You can log
-off the portal for now.
-
-\begin{center}
-\includegraphics[scale=0.6]{graphics/portal-result.png}
-\par\end{center}
-
-When your simulation is finished, the portal will send you an e-mail
-notification. Log in to the portal, click on the \texttt{Runs} icon,
-where there is a list of finished and unfinished runs. Click on the
-finished run, and you will see a list of output. Click on the \texttt{specfem3dglobe.tar.gz}
-link to download the tar file. Expand the file:
-\begin{lyxcode}
-\$~gunzip~-c~specfem3dglobe.tar.gz~|~tar~xf~-
-\end{lyxcode}
-You will find the synthetic seismograms \texttt{{*}.sem.sac} in the
-directory \texttt{OUTPUT\_FILES/}.
-
-
-\subsection{Discussion}
-
-The dimensional value of total temperature contrast across the mantle
-is derived from the Rayleigh number in Equation \ref{eq:Ra, Rayleigh number}
-and the dimensional parameters in the \texttt{{[}CitcomS.solver.const{]}}
-section. In the very beginning of the simulation, the total temperature
-contrast across the mantle is displayed on the screen. This value
-will be used to scale the non-dimensional temperature when converting
-the temperature anomaly to seismic velocities.
-\begin{lyxcode}
-Total~temperature~contrast~=~3934.055176~K
-\end{lyxcode}
-The event and stations are all on the equatorial plane. Figure \ref{fig:cookbook10}
-shows the temperature field of the equatorial slice. A large warm
-upwelling is beneath $60^{\circ}$E. We should be able to observe
-its effect on delaying teleseismic waves in the $70^{\circ}$ to $90^{\circ}$
-range.
-
-\noindent \begin{center}
-\begin{figure}[H]
-\begin{centering}
-\includegraphics[scale=0.6]{graphics/cookbook10.png}
-\par\end{centering}
-
-\caption{\label{fig:cookbook10}The equatorial slice of temperature from the
-CitcomS result. Three S wave paths probing the mantle are shown. }
-\end{figure}
-
-\par\end{center}
-
-The synthetic seismograms need to be post-processed. The post-processing
-programs we will use can be downloaded from the portal. Follow the
-instructions on the portal to build the programs. We will band-pass
-filter within the period of 30 and 500 seconds, and convolve the synthetics
-with a gaussian source time function of 50 seconds half duration,
-and append \texttt{conv} to the output filenames.
-\begin{lyxcode}
-\$~process\_syn.pl~-S~-t~30/500~-h~50~-x~conv~{*}.sac
-\end{lyxcode}
-Optionally, you can rotate the synthetics from East-North components
-to Transversal-Radial components.
-\begin{lyxcode}
-\$~rotate.pl~{*}LHE{*}.conv
-\end{lyxcode}
-
\part{Appendices}
\appendix
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