[cig-commits] r14904 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Wed May 6 14:47:57 PDT 2009
Author: tan2
Date: 2009-05-06 14:47:57 -0700 (Wed, 06 May 2009)
New Revision: 14904
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Add apt-get and yum commands to install required dependency. Add file formats for domain, coord_bin, and seismic output.
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2009-05-06 20:41:08 UTC (rev 14903)
+++ doc/CitcomS/manual/citcoms.lyx 2009-05-06 21:47:57 UTC (rev 14904)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -1953,11 +1953,50 @@
\end_layout
\begin_layout Itemize
-Python 2.3 or greater (Python 2.4 or greater is required on 64-bit machines),
- including header files, if using Pyre.
+If using Pyre: Python 2.3 or greater (Python 2.4 or greater is required on
+ 64-bit machines), including header files (Python.h).
\end_layout
\begin_layout Standard
+You can install all the dependencies in one command on most Linux machines.
+ On Debian, Ubuntu or similar distributions, use this command (as
+\family typewriter
+root
+\family default
+):
+\end_layout
+
+\begin_layout LyX-Code
+$ apt-get install build-essential python-dev
+\backslash
+
+\newline
+ openmpi-dev openmpi-bin
+\end_layout
+
+\begin_layout Standard
+On Red Hat, Fedora, CentOS, OpenSuSE or similar distributions, use this
+ command (as
+\family typewriter
+root
+\family default
+):
+\end_layout
+
+\begin_layout LyX-Code
+$ yum install make automake gcc gcc-c++ kernel-devel
+\backslash
+
+\newline
+ python python-devel openmpi openmpi-libs openmpi-devel
+\end_layout
+
+\begin_layout Standard
+On Mac OS X, Python is installed by default.
+ You will need to install a C compiler and MPI library (see sections below).
+\end_layout
+
+\begin_layout Standard
MPI installations are typically configured for a particular compiler, and
provide a special wrapper command to invoke the right compiler.
Therefore, the choice of MPI implementation often determines which C compiler
@@ -2219,8 +2258,8 @@
\family default
) in addition to the core Python package -- even if you don't plan on doing
any Python software development.
- The development package contains the Python header files, which are necessary
- for building CitcomS.
+ The development package contains the Python header files (Python.h), which
+ are necessary for building CitcomS.
\end_layout
\begin_layout Standard
@@ -2631,36 +2670,9 @@
\family typewriter
configure
\family default
- will download missing Python packages from the Internet.
-\end_layout
-
-\begin_layout Standard
-(TODO) CitcomS 3.0 requires Pythia v0.8.1 or higher, which
+ will download missing Python packages from the Internet and store them
+ under
\family typewriter
-configure
-\family default
- downloads directly from CIG.
- (Pythia v0.8.1.x is distinct from Pythia v0.8, which you may have installed
- previously.) Pythia v0.8.1.x is pure Python, and resides in a file or directory
- with the extension
-\family typewriter
-.egg
-\family default
- (e.g.,
-\family typewriter
-pythia-0.8.1.0.egg
-\family default
-).
- The
-\family typewriter
-configure
-\family default
- script may download other
-\family typewriter
-.egg
-\family default
- packages, in addition to Pythia, and store them under
-\family typewriter
\shape italic
\emph on
deps/
@@ -4083,6 +4095,16 @@
\family default
file is an XML file that specifies parameter values in a highly structured
format.
+ XML files are intended to be read and written by machines, not edited manually
+ by humans.
+ The
+\family typewriter
+.pml
+\family default
+ file format is intended for applications in which CitcomS input files are
+ generated by another program, e.g., a GUI, web application, or a high-level
+ structured editor.
+ This file fomat will not be discussed or used further in the manual.
It is composed of nested sections which are formatted as follows:
\end_layout
@@ -4102,19 +4124,6 @@
</component>
\end_layout
-\begin_layout Standard
-XML files are intended to be read and written by machines, not edited manually
- by humans.
- The
-\family typewriter
-.pml
-\family default
- file format is intended for applications in which CitcomS input files are
- generated by another program, e.g., a GUI, web application, or a high-level
- structured editor.
- This file fomat will not be discussed further here.
-\end_layout
-
\begin_layout Subsection
Specification and Placement of Configuration Files
\end_layout
@@ -9708,9 +9717,9 @@
\begin_layout Standard
This example solves for thermo-chemical convection within a full spherical
shell domain.
- Composition heterogenity exists in the Earth mantle.
- The density anomalies due to the composition heterogenity, as well as due
- to the thermal heterogeneity, drive the convection flow.
+ 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.
\end_layout
@@ -10881,12 +10890,15 @@
\begin_layout Standard
Finally, the net angular momentum of the velocity solution is removed.
- For incompressible case, the reference density does not change with the
- radius, and the net angular momentum would be equivalent to the rigid body
- rotation.
- The net angular momentum and the mode of rigid body rotation are unconstrained
- by the Stokes equation, if free-slip boundary conditions are used for the
- top and bottom boundaries in a full spherical model.
+ The net angular momentum and rigid body rotation are unconstrained by the
+ Stokes equations, if free-slip boundary conditions are used for the top
+ and bottom boundaries in a full spherical model.
+ That is, you can add an arbitrary amount of rotation to the velocity solution,
+ and the resultant velocity is still a valid solution of the Stokes equations.
+ Since no external torque is applied to the mantle in free-slip boundary
+ conditions, the angular momemtum must be constant in time.
+ Enforcing the angular momentum to be zero by removing it from the velocity
+ solution is often desirable.
\end_layout
@@ -10898,7 +10910,7 @@
\begin_layout Standard
However, for models with imposed plate velocity, it is advisable to turn
- off
+ off both
\family typewriter
remove_rigid_rotation
\family default
@@ -11305,8 +11317,12 @@
\begin_layout Standard
The embedded solver (esolver) is nested within the domain of the containing
solver (csolver).
- Both solvers are instances of a regional CitcomS solver.
- The containing solver can be a full CitcomS solver.
+ The containing solver can be either a full CitcomS solver or a regional
+ one.
+ The embedded solver can only be a regional one.
+ Both solvers are instances of a regional CitcomS solver in the cookbook
+ example.
+
\end_layout
\begin_layout LyX-Code
@@ -11351,8 +11367,8 @@
\end_layout
\begin_layout Enumerate
-The containing solver interpolates the velocity and temperature onto the
- boundary of the embedded model.
+The containing solver interpolates the velocity, stress and temperature
+ onto the boundary of the embedded model.
\end_layout
\begin_layout Enumerate
@@ -11415,13 +11431,15 @@
The containing coupler and controller (ccoupler and ccontroller) are associated
with the csolver, and the embedded coupler and controller (ecoupler and
econtroller) with the esolver.
- Each of the two solvers will track its own number of time steps.
+ Each solvers will track its own number of time steps.
The esolver has a smaller time-step size and, hence, a larger number of
time steps.
The model will finish when either of the solvers reaches the 200th time
step.
The csolver will output for every 2 steps and the esolver for every 10
steps.
+ Additional output will occur when the embedded solver is at proceduer 4
+ above.
\end_layout
\begin_layout LyX-Code
@@ -11499,10 +11517,6 @@
\end_layout
\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
Plate motion is imposed on top of the esolver, which has a mid-ocean ridge
with a 5 cm/yr half-spreading rate.
A transform fault cuts through the ridge.
@@ -12048,6 +12062,96 @@
\end_layout
+\begin_layout Section
+Cookbook 10: Generating Synthetic Seismograms from Mantle Convection Models
+\end_layout
+
+\begin_layout Subsection
+Problem
+\end_layout
+
+\begin_layout Standard
+This example is a step-up of Cookbook
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-7:-The"
+
+\end_inset
+
+, 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 from the model.
+\end_layout
+
+\begin_layout Subsection
+Solution
+\end_layout
+
+\begin_layout Standard
+Most of the parameters is copied from Cookbook
+\begin_inset LatexCommand ref
+reference "fig:Cookbook-7:-The"
+
+\end_inset
+
+.
+ We will highlight a few differences.
+ We will use a higher Rayleigh number
+\end_layout
+
+\begin_layout LyX-Code
+rayleigh = 1e9
+\end_layout
+
+\begin_layout Standard
+We will convert the temperature and composition fields to seismic velocities
+\end_layout
+
+\begin_layout LyX-Code
+[CitcomS.solver.output]
+\end_layout
+
+\begin_layout LyX-Code
+output_optional = tracer, comp_nd, seismic
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+[CitcomS.solver.param]
+\end_layout
+
+\begin_layout LyX-Code
+mineral_physics_model = 3
+\end_layout
+
+\begin_layout Standard
+(TODO)
+\end_layout
+
+\begin_layout Subsubsection
+Example: Generating Synthetic Seismograms from Mantle Convection Model,
+ cookbook10.cfg
+\end_layout
+
+\begin_layout Subsection
+Discussion
+\end_layout
+
+\begin_layout Standard
+The temperature
+\end_layout
+
+\begin_layout LyX-Code
+Total temperature contrast = 3934.055176 K
+\end_layout
+
\begin_layout Part
Appendices
\end_layout
@@ -23739,6 +23843,129 @@
adiabatic_heating viscous_heating latent_heating
\end_layout
+\begin_layout Subsection
+Domain Output (
+\family typewriter
+\size normal
+test-case.domain
+\family default
+\size default
+)
+\end_layout
+
+\begin_layout Standard
+This file is only outputted at the 0th time step.
+ This file is output by rank-0 processor only.
+ It contains the domain bounds of all processors in binary format.
+ The file begins with four intergers:
+\family typewriter
+nproc
+\family default
+,
+\family typewriter
+ncolumns
+\family default
+,
+\family typewriter
+const1
+\family default
+,
+\family typewriter
+const2
+\family default
+, where
+\family typewriter
+nproc
+\family default
+ is the number of processors,
+\family typewriter
+ncolumns
+\family default
+ is 10,
+\family typewriter
+const1
+\family default
+ and
+\family typewriter
+const2
+\family default
+ are used to detect binary incompatibility.
+ The rest of the file has
+\family typewriter
+nproc
+\family default
+
+\begin_inset Formula $\times$
+\end_inset
+
+
+\family typewriter
+ncolumns
+\family default
+ doubles, the columns contains the min/max of radius and the
+\begin_inset Formula $\theta,\phi$
+\end_inset
+
+ coordinates of the four corners:
+\end_layout
+
+\begin_layout LyX-Code
+r_min r_max theta0 phi0 theta1 phi1 theta2 phi2 theta3 phi3
+\end_layout
+
+\begin_layout Subsection
+Coordinate Binary Output (
+\family typewriter
+\size normal
+test-case.coord_bin.0
+\family default
+\size default
+)
+\end_layout
+
+\begin_layout Standard
+These files are only outputted at the 0th time step.
+ These files contain the coordinates of nodes in binary format.
+ The file begins with four intergers:
+\family typewriter
+nodex
+\family default
+,
+\family typewriter
+nodey
+\family default
+,
+\family typewriter
+nodez
+\family default
+,
+\family typewriter
+const
+\family default
+, then followed by the
+\begin_inset Formula $\theta,\phi,r$
+\end_inset
+
+ coordinates of all nodes.
+\end_layout
+
+\begin_layout Subsection
+Seismic Output (
+\family typewriter
+\size normal
+test-case.seismic.0.10
+\family default
+\size default
+)
+\end_layout
+
+\begin_layout Standard
+These files contain the density, P wave velocity and S wave velocity in
+ binary format.
+ The density of all nodes is stored in double, then followed by P wave velocity
+ of all nodes, and finally S wave velocity of all nodes.
+\end_layout
+
\begin_layout Section
HDF5 Output (
\family typewriter
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