[cig-commits] r14971 - in doc/CitcomS/manual: . graphics
tan2 at geodynamics.org
tan2 at geodynamics.org
Sun May 10 16:42:46 PDT 2009
Author: tan2
Date: 2009-05-10 16:42:46 -0700 (Sun, 10 May 2009)
New Revision: 14971
Added:
doc/CitcomS/manual/graphics/cookbook10.png
doc/CitcomS/manual/graphics/portal-param-a.png
doc/CitcomS/manual/graphics/portal-result.png
doc/CitcomS/manual/graphics/portal-run-a.png
doc/CitcomS/manual/graphics/portal-submit2-a.png
doc/CitcomS/manual/graphics/portal-upload-a.png
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
- shrunk pyre section
- added "walltime" to scheduler example
- added page separator between cookbooks, this will make the layout of each cookbook independent from each other.
- finished bookbook 10
- added binary file format
- added reference to Trampert et al 2001.
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2009-05-10 23:18:05 UTC (rev 14970)
+++ doc/CitcomS/manual/citcoms.lyx 2009-05-10 23:42:46 UTC (rev 14971)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -649,7 +649,38 @@
\end_layout
\begin_layout Standard
-This release of CitcomS 3.1 contains TODO...
+This release of CitcomS 3.1 adds the ability to convert temperature and compositi
+on to seismic velocities.
+ The seismic velocities output can be uploaded to CIG seismic portal for
+ SPECFEM3D simulation to generate synthetic seismograms.
+ Other enhancements includes: Allowing tracers in global model with nproc
+ > 2 by changing the mesh slightly; The convergence of Stokes solver is
+ controlled by parameter "accuracy" in [CitcomS.solver.vsolver].
+ "tole_compressibility" is not used anymore.
+ Also, the norms of div(u), u, and p are no longer dependent on the grid
+ size; Adding self-gravitational effect on geoid and adding Consistent-Boundary-
+Flux (CBF) method to compute dynamic topography, contributed by Shijie Zhong;
+ Adding GMT/netcdf grd input for surface velocity boundary conditions, initial
+ temperature, material dependence and local Rayleigh number in surface layers,
+ contributed by Thorsten Becker; Adding capability to read in time- and
+ geographic-dependent, top surface temperature boundary conditions, contributed
+ by Mike Gurnis; Allowing multi-component chemical viscosity; Optimizing
+ the speed.
+ Cookbook 8 becomes 13% faster than v3.0; Moving input parameter "mantle_temp"
+ from [CitcomS.solver.param] to [CitcomS.solver.ic] section.
+ Several bugs are fixed.
+ Important bug fixes include: A memory bug in visual/project_geoid.c, fixed
+ by Thorsten Becker; Initial temperature "tic_method=0" for regional model
+ applied sinusoidal perturbations to 0th processor only; Initial temperature
+ "tic_method=1" for regional model generated a top thermal boundary layer
+ 25x older than specfied by "half_space_age"; Compiling with both HDF5 and
+ Exchanger support will crash Cookbook 9 (Issue 528); Insufficient error
+ checking when reading input files (Issue 265, reported by Clint Conrad);
+ Installation bug: Python.h and system header not properly checked by configure
+ script (Isse 45, reported by Vlad Manea and Ricardo Arevalo); Manual fixes:
+ description of rheol=4 (Isse 152, reported by James Robert), energy equation
+ (Issue 162 & 164, reported by Dan Bower), documented all "tic_method" and
+ "rheol" options.
\end_layout
\begin_layout Section
@@ -668,41 +699,6 @@
\end_layout
\begin_layout Standard
-Pyre is a framework, a combination of software and design philosophy that
- promotes the reuse of code.
- In their canonical software design book,
-\emph on
-Design Patterns
-\emph default
-, Erich Gamma
-\emph on
-et al
-\emph default
- condense the concept of a framework concept down to, ``When you use a framework
-, you reuse the main body and write the code it calls.'' In the context of
- frameworks and object-oriented programming, Pyre can be thought of as a
- collection of classes and the way their instances interact.
- Programming applications based on Pyre will look similar to those written
- in any other object-oriented language.
- The Pyre framework contains a subset of parts that make up the overall
- framework.
- Each of those parts is designed to solve a specific problem.
-
-\end_layout
-
-\begin_layout Standard
-The framework approach to computation offers many advantages.
- It permits the exchange of codes and promotes the reuse of standardized
- software while preserving efficiency.
- Frameworks are also an efficient way to handle changes in computer architecture.
- They present programmers and scientists with a unified and well-defined
- task and allow for shared costs of the housekeeping aspects of software
- development.
- They provide greater institutional continuity to model development than
- piecemeal approaches.
-\end_layout
-
-\begin_layout Standard
The Pyre framework incorporates features aimed at enabling the scientific
non-expert to perform tasks easily without hindering the expert.
Target features for end users allow complete and intuitive simulation specifica
@@ -713,53 +709,6 @@
\end_layout
-\begin_layout Standard
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Description
-\begin_inset LatexCommand label
-name "Pyre-Architecture"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename graphics/c_fig1.eps
- scale 85
- rotateOrigin center
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Pyre Architecture.
- The integration framework is a set of cooperating abstract services.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
Pyre and CitcomS
\end_layout
@@ -785,12 +734,6 @@
\end_layout
-\begin_layout Standard
-This version of CitcomS ``attaches'' to Pyre via the use of bindings.
- They are included with CitcomS, eliminating the need for users to write
- or alter them.
-\end_layout
-
\begin_layout Section
Governing Equations
\begin_inset LatexCommand label
@@ -1302,11 +1245,11 @@
\begin_inset Formula $R_{0}$
\end_inset
- is about twice the layer thickness, our
+ is slightly more than twice the layer thickness, our
\begin_inset Formula $Ra$
\end_inset
- are about a factor of 8 larger than by the usual definition.
+ is about a factor of 10 larger than by the usual definition.
The phase-change Rayleigh number,
\begin_inset Formula $Rab$
\end_inset
@@ -5154,7 +5097,10 @@
\end_layout
\begin_layout LyX-Code
-queue = normal ; default queue for jobs
+queue = normal ; default queue for jobs
+\newline
+walltime = 5*minute
+ ; run time limit of the job
\end_layout
\begin_layout Standard
@@ -7926,8 +7872,13 @@
the Conjugate Gradient velocity solver.
Cookbook 8 introduces compressible convection problem, checkpointing/restarting
, geoid and tuning of the Multigrid and Uzawa velocity solver.
- Cookbook 10 introduces embedding one CitcomS domain within another CitcomS
+ 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 velocitie
+s and how to generate synthetic seismograms using SPECFEM3D_GLOBE at CIG
+ seismic portal.
+\newpage
+
\end_layout
\begin_layout Section
@@ -8196,6 +8147,12 @@
of both MPI and Pyre.
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 2: Domain Size and Velocity Boundary Conditions
\end_layout
@@ -8511,6 +8468,12 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 3: Temperature-Dependent Viscosity
\end_layout
@@ -8858,6 +8821,12 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 4: Regionally Refined Meshes
\end_layout
@@ -9094,6 +9063,12 @@
the lower resolution for the wide thermal downwelling region.
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 5: Subduction Models with Trench Rollback
\end_layout
@@ -9484,6 +9459,12 @@
slab at the other side.
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 6: Pseudo-Free-Surface Formulation
\end_layout
@@ -9706,6 +9687,12 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 7: Thermo-Chemical Convection
\end_layout
@@ -10405,6 +10392,12 @@
A model of higher resolution will not have this kind of artifact.
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 8: Compressible Steady-State Convection
\end_layout
@@ -11267,6 +11260,12 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
Cookbook 9: Nested Solver Coupling for Ridge-Plume Interaction
\end_layout
@@ -12029,7 +12028,7 @@
\align center
\begin_inset Graphics
filename graphics/cookbook9.png
- scale 60
+ width 60page%
\end_inset
@@ -12062,8 +12061,14 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Section
-Cookbook 10: Generating Synthetic Seismograms from Mantle Convection Models
+Cookbook 10: Synthetic Seismograms from Mantle Convection Models
\end_layout
\begin_layout Subsection
@@ -12084,7 +12089,7 @@
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 from the model.
+ seismograms using SPECFEM3D_GLOBE.
\end_layout
\begin_layout Subsection
@@ -12092,6 +12097,33 @@
\end_layout
\begin_layout Standard
+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
+\begin_inset LatexCommand htmlurl
+name "link"
+target "geodynamics.org/cig/software/packages/seismo/specfem3d-globe/"
+
+\end_inset
+
+ and install it on your machine, which requires a Fortran 90 compiler and
+ a cluster, or you can go to
+\begin_inset LatexCommand htmlurl
+name "CIG seismic portal"
+target "crust.geodynamics.org/portals/seismo/"
+
+\end_inset
+
+ to launch a job, which only requires a browser.
+ We will use the later approach in the cookbook.
+\end_layout
+
+\begin_layout Subsubsection
+Running CitcomS
+\end_layout
+
+\begin_layout Standard
Most of the parameters are copied from Cookbook
\begin_inset LatexCommand ref
reference "fig:Cookbook-7:-The"
@@ -12100,7 +12132,7 @@
.
We will highlight a few differences.
- We use a higher Rayleigh number
+ We use a higher Rayleigh number.
\end_layout
\begin_layout LyX-Code
@@ -12108,50 +12140,977 @@
\end_layout
\begin_layout Standard
-and convert the temperature and composition fields to seismic velocities
+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.)
\end_layout
\begin_layout LyX-Code
-[CitcomS.solver.output]
+radius_inner = 0.546
\end_layout
+\begin_layout Standard
+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
+\shape italic
+Trampert, Vacher, and Vlaar
+\shape default
+
+\begin_inset LatexCommand cite
+key "Trampert mineral physics model 2001"
+
+\end_inset
+
+.
+ In their paper, the (depth dependent) temperature and composition derivates
+ 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 over-stretching the model, but we are using it for demonstration
+ purpose.
+\end_layout
+
\begin_layout LyX-Code
+mineral_physics_model = 3
+\end_layout
+
+\begin_layout Standard
+We will output the converted density and seismic velocities for SPECFEM3D_GLOBE
+ consumption.
+ This option enables the binary seismic output (
+\family typewriter
+*.seismic.*
+\family default
+ files), as well as other binary output (
+\family typewriter
+*.domain
+\family default
+ and
+\family typewriter
+*.coord_bin.*
+\family default
+ files) that SPECFEM3D_GLOBE will read.
+ The formats of these binary files are provided in Appendix
+\begin_inset LatexCommand ref
+reference "sec:Misc.-Binary-Output"
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout LyX-Code
output_optional = tracer, comp_nd, seismic
\end_layout
+\begin_layout Subsubsection
+Example: Synthetic Seismograms from Mantle Convection Model, cookbook10.cfg
+\end_layout
+
\begin_layout LyX-Code
+# Cookbook 10: Synthetic Seismograms from Mantle Convection Models
+\end_layout
+\begin_layout LyX-Code
+[CitcomS]
\end_layout
\begin_layout LyX-Code
+solver = full
+\end_layout
+
+\begin_layout LyX-Code
+steps = 15
+\newline
+
+\newline
+[CitcomS.controller]
+\end_layout
+
+\begin_layout LyX-Code
+monitoringFrequency = 5
+\newline
+
+\newline
+[CitcomS.solver]
+\end_layout
+
+\begin_layout LyX-Code
+datadir = output
+\end_layout
+
+\begin_layout LyX-Code
+datafile = cookbook10
+\end_layout
+
+\begin_layout LyX-Code
+rayleigh = 1e9
+\newline
+
+\newline
+[CitcomS.solver.mesher]
+\end_layout
+
+\begin_layout LyX-Code
+radius_inner = 0.546
+\newline
+
+\newline
+[CitcomS.solver.ic]
+\end_layout
+
+\begin_layout LyX-Code
+num_perturbations = 1
+\end_layout
+
+\begin_layout LyX-Code
+perturbl = 3
+\end_layout
+
+\begin_layout LyX-Code
+perturbm = 2
+\end_layout
+
+\begin_layout LyX-Code
+perturblayer = 5
+\end_layout
+
+\begin_layout LyX-Code
+perturbmag = 0.05
+\newline
+
+\newline
+[CitcomS.solver.output]
+\end_layout
+
+\begin_layout LyX-Code
+output_optional = tracer,comp_nd,seismic
+\newline
+
+\newline
[CitcomS.solver.param]
\end_layout
\begin_layout LyX-Code
mineral_physics_model = 3
+\newline
+
+\newline
+[CitcomS.solver.tracer]
\end_layout
-\begin_layout Standard
-(TODO)
+\begin_layout LyX-Code
+tracer = on
\end_layout
+\begin_layout LyX-Code
+tracer_ic_method = 0
+\end_layout
+
+\begin_layout LyX-Code
+tracers_per_element = 20
+\end_layout
+
+\begin_layout LyX-Code
+tracer_file = tracer.dat
+\newline
+
+\newline
+tracer_flavors = 2
+\end_layout
+
+\begin_layout LyX-Code
+ic_method_for_flavors = 0
+\end_layout
+
+\begin_layout LyX-Code
+z_interface = 0.7
+\newline
+
+\newline
+chemical_buoyancy = 1
+\end_layout
+
+\begin_layout LyX-Code
+buoy_type = 1
+\end_layout
+
+\begin_layout LyX-Code
+buoyancy_ratio = 0.5
+\newline
+
+\newline
+regular_grid_deltheta = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+regular_grid_delphi = 1.0
+\newline
+
+\newline
+[CitcomS.solver.vsolver]
+\end_layout
+
+\begin_layout LyX-Code
+Solver = cgrad
+\end_layout
+
+\begin_layout LyX-Code
+accuracy = 1e-04
+\end_layout
+
+\begin_layout LyX-Code
+vlowstep = 1000
+\end_layout
+
+\begin_layout LyX-Code
+piterations = 1000
+\newline
+
+\newline
+# Assign the viscosities.
+\end_layout
+
+\begin_layout LyX-Code
+[CitcomS.solver.visc]
+\end_layout
+
+\begin_layout LyX-Code
+VISC_UPDATE = on
+\end_layout
+
+\begin_layout LyX-Code
+num_mat = 4
+\end_layout
+
+\begin_layout LyX-Code
+visc0 = 1,1,1,1
+\end_layout
+
+\begin_layout LyX-Code
+TDEPV = on
+\end_layout
+
+\begin_layout LyX-Code
+rheol = 4
+\end_layout
+
+\begin_layout LyX-Code
+viscE = 0.2,0.2,0.2,0.2
+\end_layout
+
+\begin_layout LyX-Code
+viscT = 0,0,0,0
+\end_layout
+
+\begin_layout LyX-Code
+viscZ = 0,0,0,0
+\end_layout
+
+\begin_layout LyX-Code
+VMIN = on
+\end_layout
+
+\begin_layout LyX-Code
+visc_min = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+VMAX = on
+\end_layout
+
+\begin_layout LyX-Code
+visc_max = 100.0
+\end_layout
+
\begin_layout Subsubsection
-Example: Generating Synthetic Seismograms from Mantle Convection Model,
- cookbook10.cfg
+Running SPECFEM3D_GLOBE from CIG Seismic Portal
\end_layout
+\begin_layout Standard
+Using your favorite browser, go to the homepage of
+\begin_inset LatexCommand htmlurl
+name "CIG seismic portal"
+target "crust.geodynamics.org/portals/seismo/"
+
+\end_inset
+
+.
+ Free registration is required to use the portal.
+ Your initial account has 10,000 SUs (CPU-hours) allocated.
+ A short (20 minute 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.
+\end_layout
+
+\begin_layout Standard
+After you login to the portal, take a few minutes to read the instruction
+ and familiar yourself with the interface.
+ You will see a toolbar with big icons on the top and several gray-out tabs
+ below the toolbar.
+ The toolbar allows you to specify the earthquake source (
+\family typewriter
+Events
+\family default
+), the receivers (
+\family typewriter
+Stations
+\family default
+), and simulation parameters (
+\family typewriter
+3D Parameters
+\family default
+), including the resolution (
+\family typewriter
+Mesh
+\family default
+) and the seismic velocity model for the crust and mantle (
+\family typewriter
+3D Models
+\family default
+).
+ In the cookbook, we will upload the result of CitcomS as a 3D Model and
+ upload our own fictitious stations and event.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename graphics/portal-upload-a.png
+ lyxscale 75
+ scale 60
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Click on the
+\family typewriter
+3D Models
+\family default
+ icon (1), and the
+\family typewriter
+Upload
+\family default
+ tab (2), then click on the link
+\family typewriter
+citcoms_isotropic_no_crust.tgz
+\family default
+ (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 overlaid by 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 Pacific and where is
+ Asia, we do not want to impose a 3D crust model.
+ You can untar the file by running:
+\end_layout
+
+\begin_layout LyX-Code
+$ gunzip
+\family typewriter
+-c citcoms_isotropic_no_crust.tgz | tar xf -
+\end_layout
+
+\begin_layout Standard
+You will supply the CitcomS output to the code.
+ Copy these CitcomS output files
+\family typewriter
+cookbook.domain
+\family default
+,
+\family typewriter
+cookbook.coord_bin.*
+\family default
+, and
+\family typewriter
+cookbook.seismic.*.15
+\family default
+ to the directory
+\family typewriter
+citcoms_isotropic_no_crust/shared/
+\family default
+, so that the content of the directory looks like:
+\end_layout
+
+\begin_layout LyX-Code
+$ ls citcoms_isotropic_no_crust/shared/
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.0 cookbook10.seismic.0.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.1 cookbook10.seismic.10.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.10 cookbook10.seismic.11.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.11 cookbook10.seismic.1.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.2 cookbook10.seismic.2.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.3 cookbook10.seismic.3.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.4 cookbook10.seismic.4.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.5 cookbook10.seismic.5.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.6 cookbook10.seismic.6.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.7 cookbook10.seismic.7.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.8 cookbook10.seismic.8.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.coord_bin.9 cookbook10.seismic.9.15
+\end_layout
+
+\begin_layout LyX-Code
+cookbook10.domain
+\end_layout
+
+\begin_layout Standard
+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
+\family typewriter
+citcoms_isotropic_no_crust/citcoms_parm.h
+\family default
+ to become:
+\end_layout
+
+\begin_layout LyX-Code
+/* filename prefix of citcoms output */
+\end_layout
+
+\begin_layout LyX-Code
+const char citcoms_model_filename_base[] = "@THIS_DIR@/shared/cookbook10";
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+/* time step of citcoms output */
+\end_layout
+
+\begin_layout LyX-Code
+const int citcoms_step = 15;
+\end_layout
+
+\begin_layout Standard
+The portal has a few conventions on where to put the data.
+ First, the magic string
+\family typewriter
+ at THIS_DIR@
+\family default
+ 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
+ launchs the job.
+ Third, the subdirectory
+\family typewriter
+shared/
+\family default
+ is special such that files in this directory will not be distrubted to
+ all computer nodes.
+ Data files of huge size should be put in this directory.
+ You might want to edit
+\family typewriter
+citcoms_isotropic_no_crust/description.txt
+\family default
+ 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.
+\end_layout
+
+\begin_layout LyX-Code
+$ tar cf
+\family typewriter
+cookbook10.tar citcoms_isotropic_no_crust/
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+$ gzip cookbook10.tar
+\end_layout
+
+\begin_layout Standard
+Now, you can upload the data by clicking on the
+\family typewriter
+Browse
+\family default
+ button (4), choosing
+\family typewriter
+cookbook10.tar.gz
+\family default
+ from the dialogue, then clicking on the
+\family typewriter
+Upload
+\family default
+ button.
+ After the portal confirms that the upload is successful, click on the
+\family typewriter
+3D Models
+\family default
+ icon again, you will see
+\family typewriter
+cookbook10
+\family default
+ is among the available 3D models.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename graphics/portal-param-a.png
+ lyxscale 75
+ scale 60
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+You have to select a few parameters for a SPECFEM3D_GLOBE run.
+ Click on the
+\family typewriter
+3D Parameters
+\family default
+ icon (5), the
+\family typewriter
+New
+\family default
+ tab (6), and 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 wave of
+ 27 second period.
+ Since CitcomS mesh is a perfect sphere, you need to disable
+\family typewriter
+topography
+\family default
+ and
+\family typewriter
+ellipticity
+\family default
+ to have a matching mesh in SPECFEM3D_GLOBE.
+ The
+\family typewriter
+oceans
+\family default
+ is disabled because we don't have 3D crust.
+\end_layout
+
+\begin_layout Standard
+We will provide our own fictitious earthquake source and seismic stations.
+ The earthquake source is defined in
+\family typewriter
+cmt-solution.cookbook10
+\family default
+ in the cookbook directory.
+ The source is located at 15 km depth of
+\begin_inset Formula $0^{\circ}$
+\end_inset
+
+N,
+\begin_inset Formula $0^{\circ}$
+\end_inset
+
+E
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+.
+ The half duration of the source is 0 second, which means a step function
+ is used.
+ Click on the
+\family typewriter
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+Events
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+ icon and the
+\family typewriter
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+upload
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+ tab to upload the file
+\family typewriter
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+cmt-solution.cookbook10
+\family default
+.
+ The stations are defined in
+\family typewriter
+stations.cookbook10
+\family default
+ in the cookbook directory.
+ The stations are on the Equator and is 70 to 100 degree away from the source.
+
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+Click on the
+\family typewriter
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+Stations
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+ icon and the
+\family typewriter
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+upload
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+ tab to upload the file
+\family typewriter
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
+stations.cookbook10
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename graphics/portal-run-a.png
+ lyxscale 60
+ scale 75
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Finally, we are ready to launch a SPECFEM3D_GLOBE simulation.
+ Click on the
+\family typewriter
+Runs
+\family default
+ icon (7), then the
+\family typewriter
+New
+\family default
+ tab (8), select our recectly uploaded event, stations and parameters.
+ Set the record length to 30 minutes, which will give us synthetic seismograms
+ of 30 minutes.
+ Click the
+\family typewriter
+Save
+\family default
+ button to save the settings.
+
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename graphics/portal-submit2-a.png
+ lyxscale 60
+ scale 60
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+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 review all settings, scroll to the bottom of the page.
+ Click on the
+\family typewriter
+Start
+\family default
+ button.
+ The request of simulation will be 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 now.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename graphics/portal-result.png
+ lyxscale 60
+ scale 60
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+When your simulation is finished, the portal will send you an email notification.
+ Log in to the portal, click on the
+\family typewriter
+Runs
+\family default
+ icon, there is a list of finished and unfinished runs.
+ Click on the finished run, you will see a list of output.
+ Click on the
+\family typewriter
+specfem3dglobe.tar.gz
+\family default
+ link to download the tar file.
+ Expand the file:
+\end_layout
+
+\begin_layout LyX-Code
+$ gunzip
+\family typewriter
+-c specfem3dglobe.tar.gz | tar xf -
+\end_layout
+
+\begin_layout Standard
+You will find the synthetic seismograms
+\family typewriter
+*.sem.sac
+\family default
+ in the directory
+\family typewriter
+OUTPUT_FILES/
+\family default
+.
+\end_layout
+
\begin_layout Subsection
Discussion
\end_layout
\begin_layout Standard
-The temperature
+The dimensional value of total temperature contrast across the mantle is
+ derived from the Rayleigh number in Equation
+\begin_inset LatexCommand ref
+reference "eq:Ra, Rayleigh number"
+
+\end_inset
+
+ and the dimensional parameters in
+\family typewriter
+[CitcomS.solver.const]
+\family default
+ 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 convertin
+g the temperature anomaly to seismic velocities.
\end_layout
\begin_layout LyX-Code
Total temperature contrast = 3934.055176 K
\end_layout
+\begin_layout Standard
+The event and stations are all on the equatorial plane.
+ Figure
+\begin_inset LatexCommand ref
+reference "fig:cookbook10"
+
+\end_inset
+
+ shows the temperature field of the equatorial slice.
+ A large warm upwelling is benearth
+\begin_inset Formula $60^{\circ}$
+\end_inset
+
+E.
+ We should be able to observe its effect on delaying teleseismic waves in
+
+\begin_inset Formula $70^{\circ}$
+\end_inset
+
+ to
+\begin_inset Formula $90^{\circ}$
+\end_inset
+
+range.``
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename graphics/cookbook10.png
+ lyxscale 60
+ scale 60
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:cookbook10"
+
+\end_inset
+
+The equatorial slice of temperature from CitcomS result.
+
+\begin_inset Note Comment
+status open
+
+\begin_layout Standard
+TODO: plotting composition, density and dVs slices.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The synthetic seismograms need to be post-processed.
+ The post-processing programs we will use can be downloaded from the potral.
+ Follow the instruction on 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
+\family typewriter
+conv
+\family default
+ to the output filenames.
+\end_layout
+
+\begin_layout LyX-Code
+$ process_syn.pl -S -t 30/500 -h 50 -x conv *.sac
+\end_layout
+
+\begin_layout Standard
+Optionally, you can rotate the synthetics from East-North components to
+ Transversal-Radial components.
+\end_layout
+
+\begin_layout LyX-Code
+$ rotate.pl *LHE*.conv
+\end_layout
+
\begin_layout Part
Appendices
\end_layout
@@ -23843,7 +24802,56 @@
adiabatic_heating viscous_heating latent_heating
\end_layout
+\begin_layout Section
+HDF5 Output (
+\family typewriter
+\size large
+test-case.h5
+\family default
+\size default
+)
+\end_layout
+
+\begin_layout Standard
+The format and layout of HDF5 output is described in Section
+\begin_inset LatexCommand vref
+reference "sec:Data-Layout"
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Section
+Misc.
+ Binary Output
+\begin_inset LatexCommand label
+name "sec:Misc.-Binary-Output"
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
+Checkpoint Output (
+\family typewriter
+\size normal
+test-case.checkpoint.0.10
+\family default
+\size default
+)
+\end_layout
+
+\begin_layout Standard
+These files are used for restarting the run.
+ These files are not portable.
+ You cannot run a model on machine A, copy the checkpoint files to machine
+ B, and expect you can always restart the simulation on machine B.
+ Their format is undocumented on purpose and will remain so.
+\end_layout
+
+\begin_layout Subsection
Domain Output (
\family typewriter
\size normal
@@ -23966,26 +24974,6 @@
of all nodes, and finally S wave velocity of all nodes.
\end_layout
-\begin_layout Section
-HDF5 Output (
-\family typewriter
-\size large
-test-case.h5
-\family default
-\size default
-)
-\end_layout
-
-\begin_layout Standard
-The format and layout of HDF5 output is described in Section
-\begin_inset LatexCommand vref
-reference "sec:Data-Layout"
-
-\end_inset
-
-.
-\end_layout
-
\begin_layout Chapter
\begin_inset LatexCommand label
name "cha:License"
@@ -24988,7 +25976,11 @@
Geophys.
Res.
\emph default
-, 109, B07402, doi:10.1029/2003JB002847.
+,
+\shape italic
+109
+\shape default
+, B07402, doi:10.1029/2003JB002847.
\end_layout
\begin_layout Bibliography
@@ -25009,5 +26001,28 @@
8302, doi:10.1029/2001GC000214.
\end_layout
+\begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "20"
+key "Trampert mineral physics model 2001"
+
+\end_inset
+
+Trampert, J., P.
+ Vacher, and N.
+ Vlaar (2001), Sensitivities of seismic velocities to temperature, pressure
+ and composition in the lower mantle,
+\emph on
+Phys.
+ Earth Planet.
+ Inter.
+\emph default
+,
+\shape italic
+124
+\shape default
+, 255-267.
+\end_layout
+
\end_body
\end_document
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===================================================================
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===================================================================
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