[cig-commits] r19582 - in doc/CitcomS/manual: . graphics
emheien at geodynamics.org
emheien at geodynamics.org
Thu Feb 2 14:03:54 PST 2012
Author: emheien
Date: 2012-02-02 14:03:54 -0800 (Thu, 02 Feb 2012)
New Revision: 19582
Modified:
doc/CitcomS/manual/citcoms.lyx
doc/CitcomS/manual/citcoms.pdf
doc/CitcomS/manual/graphics/citcoms_cover.pdf
doc/CitcomS/manual/graphics/citcoms_cover.psd
Log:
Updated manual for 3.2.0
Added notes about Pyre being off by default
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2012-02-02 19:05:34 UTC (rev 19581)
+++ doc/CitcomS/manual/citcoms.lyx 2012-02-02 22:03:54 UTC (rev 19582)
@@ -1,5 +1,5 @@
-#LyX 1.6.9 created this file. For more info see http://www.lyx.org/
-\lyxformat 345
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
\begin_document
\begin_header
\textclass book
@@ -12,18 +12,26 @@
\raggedbottom
\end_preamble
\use_default_options false
+\maintain_unincluded_children false
\language english
+\language_package default
\inputencoding auto
+\fontencoding global
\font_roman default
\font_sans default
\font_typewriter default
\font_default_family default
+\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
@@ -31,9 +39,18 @@
\use_geometry true
\use_amsmath 0
\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
\cite_engine basic
\use_bibtopic false
+\use_indices false
\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
\leftmargin 1in
\topmargin 1in
\rightmargin 1in
@@ -41,15 +58,16 @@
\secnumdepth 3
\tocdepth 5
\paragraph_separation indent
-\defskip medskip
+\paragraph_indentation default
\quotes_language swedish
\papercolumns 1
\papersides 2
\paperpagestyle headings
\tracking_changes false
\output_changes false
-\author ""
-\author ""
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
\end_header
\begin_body
@@ -107,7 +125,7 @@
\begin_inset Newline newline
\end_inset
-Version 3.1.1.1
+Version 3.2.0
\end_layout
\begin_layout Date
@@ -719,136 +737,134 @@
\end_layout
\begin_layout Standard
-This release of CitcomS 3.1 adds the ability to convert temperature and compositi
+The release of CitcomS 3.1 added the ability to convert temperature and compositi
on to seismic velocities.
The seismic velocities output can be uploaded to the CIG Seismology Web
Portal for SPECFEM3D simulation to generate synthetic seismograms.
- Other enhancements include:
+ Other enhancements include adding a self-gravitational effect on geoid
+ and adding the Consistent-Boundary-Flux (CBF) method to compute dynamic
+ topography, contributed by Shijie Zhong.
+ Also, GMT/NetCDF grd input was added for surface velocity boundary conditions,
+ initial temperature, material dependence and local Rayleigh number in surface
+ layers, contributed by Thorsten Becker.
+ Mike Gurnis contributed added capability to read in time- and geographic-depend
+ent, top surface temperature boundary conditions.
+ Finally, this version allows multi-component chemical viscosity.
\end_layout
-\begin_layout Itemize
-Allowing tracers in global model with nproc > 2 by changing the mesh slightly;
+\begin_layout Standard
+Some of the aforementioned features are backward-incompatible, including:
+
\end_layout
-\begin_layout Itemize
-The convergence of Stokes solver is controlled by parameter ``accuracy''
- in [CitcomS.solver.vsolver].
- ``tole_compressibility'' and ``relative_err_accuracy'' are not used anymore.
- Also, the norms of div(u), u, and p are no longer dependent on the grid
- size;
+\begin_layout Enumerate
+The global mesh is changed.
+ The coordinates of all nodes are slightly shifted laterally.
+ The change is not visually discernible, but does affect the solution compared
+ to previous versions.
+
\end_layout
-\begin_layout Itemize
-Adding a self-gravitational effect on geoid and adding the Consistent-Boundary-F
-lux (CBF) method to compute dynamic topography, contributed by Shijie Zhong;
+\begin_layout Enumerate
+The convergence criterion of the Stokes solver is changed.
+ A single parameter ``accuracy'' is used to control the accuracy of the
+ continuity and momentum equations.
+ The default value of ``accuracy'' was
+\begin_inset Formula $10^{-6}$
+\end_inset
+
+ and is now
+\begin_inset Formula $10^{-4}$
+\end_inset
+
+.
+
\end_layout
-\begin_layout Itemize
-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;
+\begin_layout Enumerate
+The input parameter ``mantle_temp'' is moved from the [CitcomS.solver.param]
+ to the [CitcomS.solver.ic] section.
\end_layout
-\begin_layout Itemize
-Adding capability to read in time- and geographic-dependent, top surface
- temperature boundary conditions, contributed by Mike Gurnis;
+\begin_layout Standard
+This release of CitcomS 3.2 adds numerous changes since 3.1.1 which was released
+ in 2009.
+ These include improved implementations of internal stress, radial layer
+ dependent viscosity, and velocity boundary conditions.
+ Improvements have also been made in solver convergence controls, VTK output
+ and several bug fixes.
+ Finally, the Pyre configuration option has been turned off by default,
+ though it can be enabled during configuration.
+ Other enhancements include:
\end_layout
\begin_layout Itemize
-Allowing multi-component chemical viscosity;
+If Python 2.7 is detected, Pyre is disabled due to conflicts.
\end_layout
\begin_layout Itemize
-Optimizing the speed.
- Cookbook 8 becomes 13% faster than v3.0;
+Trial implementation of anisotropic viscosity.
\end_layout
\begin_layout Itemize
-Better convergence for the coupled solver case;
+Added support of multigrid solver in Exchanger.
\end_layout
\begin_layout Itemize
-Moving input parameter ``mantle_temp'' from [CitcomS.solver.param] to [CitcomS.solv
-er.ic] section.
-
+Improved handling of grd-read velocity and traction boundary conditions.
\end_layout
\begin_layout Itemize
-Several bugs are fixed.
- Important bug fixes include:
+Changed default parameters for z_410, z_lmantle, z_lith to more Earth-like
+ parameters.
\end_layout
-\begin_deeper
\begin_layout Itemize
-A memory bug in visual/project_geoid.c, fixed by Thorsten Becker;
+Added test implementation of steady state strain-rate weakening via PDEPV
+ psrw=on parameter.
\end_layout
\begin_layout Itemize
-Initial temperature ``tic_method=0'' for regional model applied sinusoidal
- perturbations to 0th processor only;
+Added Murnaghan's integrated linear EoS.
\end_layout
\begin_layout Itemize
-Initial temperature ``tic_method=1'' for regional model generated a top
- thermal boundary layer 25x older than specfied by ``half_space_age'';
+Added augmented Lagrangian component of stiffness matrix in cbf topo.
\end_layout
\begin_layout Itemize
-Compiling with both HDF5 and Exchanger support will crash Cookbook 9 (Issue
- 528);
+Performance optimizations for CUDA code.
+ Contributed by Leif Strand.
\end_layout
\begin_layout Itemize
-Insufficient error checking when reading input files (Issue 265, reported
- by Clint Conrad);
+Fixed several bugs in the code and manual, including:
\end_layout
+\begin_deeper
\begin_layout Itemize
-Installation bug: Python.h and system header not properly checked by configure
- script (Isse 45, reported by Vlad Manea and Ricardo Arevalo);
+Fixed a bug in pseudo free surface, reported by Robert Moucha.
\end_layout
\begin_layout Itemize
-Manual fixes: description of rheol=4 (Issue 152, reported by James Robert),
- energy equation (Issue 162 & 164, reported by Dan Bower), documented all
- ``tic_method'' and ``rheol'' options.
+Correctly handle orphan tracers.
\end_layout
-\end_deeper
-\begin_layout Standard
-Some of the aforementioned features are backward-incompatible, including:
-
+\begin_layout Itemize
+Added Pyre binding for write_q_files, z_layer, r_grid_layers, rr, nr, others.
\end_layout
-\begin_layout Enumerate
-The global mesh is changed.
- The coordinates of all nodes are slightly shifted laterally.
- The change is not visually discernible, but does affect the solution compared
- to previous versions.
-
+\begin_layout Itemize
+Replaced fixed accuracy setting.
+ Bug reported by Rob Moucha.
\end_layout
-\begin_layout Enumerate
-The convergence criterion of the Stokes solver is changed.
- A single parameter ``accuracy'' is used to control the accuracy of the
- continuity and momentum equations.
- The default value of ``accuracy'' was
-\begin_inset Formula $10^{-6}$
-\end_inset
-
- and is now
-\begin_inset Formula $10^{-4}$
-\end_inset
-
-.
+\begin_layout Itemize
+Fixed temperature perturbation bug for multiple processors.
\end_layout
-\begin_layout Enumerate
-The input parameter ``mantle_temp'' is moved from the [CitcomS.solver.param]
- to the [CitcomS.solver.ic] section.
-\end_layout
-
+\end_deeper
\begin_layout Section
About Pyre
\end_layout
@@ -920,8 +936,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\left(\rho u_{i}\right)_{,i}=0\label{eq:conservation of mass}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\left(\rho u_{i}\right)_{,i}=0\label{eq:conservation of mass}
+\end{equation}
\end_inset
@@ -930,8 +948,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
--P_{,i}+\left(\eta(u_{i,j}+u_{j,i}-\frac{2}{3}u_{k,k}\delta_{ij})\right)_{,i}-\delta\rho g\delta_{ir}=0\label{eq:conservation of momentum}\end{equation}
+\begin_inset Formula
+\begin{equation}
+-P_{,i}+\left(\eta(u_{i,j}+u_{j,i}-\frac{2}{3}u_{k,k}\delta_{ij})\right)_{,i}-\delta\rho g\delta_{ir}=0\label{eq:conservation of momentum}
+\end{equation}
\end_inset
@@ -940,8 +960,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\rho c_{P}\left(T_{,t}+u_{i}T_{,i}\right)=\rho c_{P}\kappa T_{,ii}-\rho\alpha gu_{r}T+\Phi+\rho\left(Q_{L,t}+u_{i}Q_{L,i}\right)+\rho H\label{eq:conservation of energy}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\rho c_{P}\left(T_{,t}+u_{i}T_{,i}\right)=\rho c_{P}\kappa T_{,ii}-\rho\alpha gu_{r}T+\Phi+\rho\left(Q_{L,t}+u_{i}Q_{L,i}\right)+\rho H\label{eq:conservation of energy}
+\end{equation}
\end_inset
@@ -1052,8 +1074,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\delta\rho=-\alpha\bar{\rho}(T-\bar{T_{a}})+\delta\rho_{ph}\Gamma+\delta\rho_{ch}C\label{eq:density anomalies}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\delta\rho=-\alpha\bar{\rho}(T-\bar{T_{a}})+\delta\rho_{ph}\Gamma+\delta\rho_{ch}C\label{eq:density anomalies}
+\end{equation}
\end_inset
@@ -1112,8 +1136,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\pi=\bar{\rho}g(1-r-d_{ph})-\gamma_{ph}(T-T_{ph})\label{eq:reduced pressure}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\pi=\bar{\rho}g(1-r-d_{ph})-\gamma_{ph}(T-T_{ph})\label{eq:reduced pressure}
+\end{equation}
\end_inset
@@ -1122,8 +1148,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\Gamma=\frac{1}{2}\left(1+\tanh\left(\frac{\pi}{\bar{\rho}gw_{ph}}\right)\right)\label{eq:phase function}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\Gamma=\frac{1}{2}\left(1+\tanh\left(\frac{\pi}{\bar{\rho}gw_{ph}}\right)\right)\label{eq:phase function}
+\end{equation}
\end_inset
@@ -1167,8 +1195,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\rho=\rho_{0}\rho^{'}\label{eq:rho dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\rho=\rho_{0}\rho^{'}\label{eq:rho dim}
+\end{equation}
\end_inset
@@ -1177,8 +1207,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\alpha=\alpha_{0}\alpha^{'}\label{eq:alpha dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\alpha=\alpha_{0}\alpha^{'}\label{eq:alpha dim}
+\end{equation}
\end_inset
@@ -1187,8 +1219,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-g=g_{0}g^{'}\label{eq:g dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+g=g_{0}g^{'}\label{eq:g dim}
+\end{equation}
\end_inset
@@ -1197,14 +1231,18 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\kappa=\kappa_{0}\kappa^{'}\label{eq:kappa dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\kappa=\kappa_{0}\kappa^{'}\label{eq:kappa dim}
+\end{equation}
\end_inset
-\begin_inset Formula \begin{equation}
-\eta=\eta_{0}\eta^{'}\label{eq:eta dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\eta=\eta_{0}\eta^{'}\label{eq:eta dim}
+\end{equation}
\end_inset
@@ -1213,8 +1251,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-c_{P}=c_{P0}c_{P}^{'}\label{eq:cp dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+c_{P}=c_{P0}c_{P}^{'}\label{eq:cp dim}
+\end{equation}
\end_inset
@@ -1223,8 +1263,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-x_{i}=R_{0}x_{i}^{'}\label{eq:x dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+x_{i}=R_{0}x_{i}^{'}\label{eq:x dim}
+\end{equation}
\end_inset
@@ -1232,8 +1274,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
-u_{i}=\frac{\kappa_{0}}{R_{0}}u_{i}^{'}\label{eq:u dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+u_{i}=\frac{\kappa_{0}}{R_{0}}u_{i}^{'}\label{eq:u dim}
+\end{equation}
\end_inset
@@ -1242,8 +1286,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-T_{0}=\Delta TT_{0}'\label{eq:T0 dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+T_{0}=\Delta TT_{0}'\label{eq:T0 dim}
+\end{equation}
\end_inset
@@ -1252,8 +1298,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-T=\Delta T(T'+T_{0}')\label{eq:T dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+T=\Delta T(T'+T_{0}')\label{eq:T dim}
+\end{equation}
\end_inset
@@ -1262,8 +1310,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-t=\frac{R_{0}^{2}}{\kappa_{0}}t^{'}\label{eq:t dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+t=\frac{R_{0}^{2}}{\kappa_{0}}t^{'}\label{eq:t dim}
+\end{equation}
\end_inset
@@ -1272,8 +1322,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-H=\frac{\kappa_{0}}{R_{0}^{2}}c_{P0}\Delta TH^{'}\label{eq:H dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+H=\frac{\kappa_{0}}{R_{0}^{2}}c_{P0}\Delta TH^{'}\label{eq:H dim}
+\end{equation}
\end_inset
@@ -1282,14 +1334,18 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-P=\frac{\eta_{0}\kappa_{0}}{R_{0}^{2}}P^{'}\label{eq:p dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+P=\frac{\eta_{0}\kappa_{0}}{R_{0}^{2}}P^{'}\label{eq:p dim}
+\end{equation}
\end_inset
-\begin_inset Formula \begin{equation}
-d_{ph}=R_{0}d_{ph}^{'}\label{eq:dph dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+d_{ph}=R_{0}d_{ph}^{'}\label{eq:dph dim}
+\end{equation}
\end_inset
@@ -1298,8 +1354,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\gamma_{ph}=\frac{\rho_{0}g_{0}R_{0}}{\Delta T}\gamma_{ph}^{'}\label{eq:gammaph dim}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\gamma_{ph}=\frac{\rho_{0}g_{0}R_{0}}{\Delta T}\gamma_{ph}^{'}\label{eq:gammaph dim}
+\end{equation}
\end_inset
@@ -1349,8 +1407,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
-u_{i,i}+\frac{1}{\bar{\rho}}\frac{d\bar{\rho}}{dr}u_{r}=0\label{eq:non-dimensional continuity eqn}\end{equation}
+\begin_inset Formula
+\begin{equation}
+u_{i,i}+\frac{1}{\bar{\rho}}\frac{d\bar{\rho}}{dr}u_{r}=0\label{eq:non-dimensional continuity eqn}
+\end{equation}
\end_inset
@@ -1358,8 +1418,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
--P_{,i}+\left(\eta(u_{i,j}+u_{j,i}-\frac{2}{3}u_{k,k}\delta_{ij})\right)_{,i}+(Ra\bar{\rho}\alpha T-Ra_{b}\Gamma-Ra_{c}C)g\delta_{ir}=0\label{eq:non-dimensional momentum eqn}\end{equation}
+\begin_inset Formula
+\begin{equation}
+-P_{,i}+\left(\eta(u_{i,j}+u_{j,i}-\frac{2}{3}u_{k,k}\delta_{ij})\right)_{,i}+(Ra\bar{\rho}\alpha T-Ra_{b}\Gamma-Ra_{c}C)g\delta_{ir}=0\label{eq:non-dimensional momentum eqn}
+\end{equation}
\end_inset
@@ -1368,10 +1430,13 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
+\begin_inset Formula
+\begin{equation}
\begin{array}{c}
\bar{\rho}c_{P}\left(T_{,t}+u_{i}T_{,i}\right)\left(1+2\Gamma\left(1-\Gamma\right)\frac{\gamma_{ph}^{2}}{d_{ph}}\frac{Ra_{b}}{Ra}Di\left(T+T_{0}\right)\right)=\bar{\rho}c_{P}\kappa T_{,ii}\\
--\bar{\rho}\alpha gu_{r}Di\left(T+T_{0}\right)\left(1+2\Gamma\left(1-\Gamma\right)\frac{\gamma_{ph}}{d_{ph}}\frac{Ra_{b}}{Ra}\right)+\frac{Di}{Ra}\Phi+\bar{\rho}H\end{array}\label{eq:non-dimensional energy eqn}\end{equation}
+-\bar{\rho}\alpha gu_{r}Di\left(T+T_{0}\right)\left(1+2\Gamma\left(1-\Gamma\right)\frac{\gamma_{ph}}{d_{ph}}\frac{Ra_{b}}{Ra}\right)+\frac{Di}{Ra}\Phi+\bar{\rho}H
+\end{array}\label{eq:non-dimensional energy eqn}
+\end{equation}
\end_inset
@@ -1389,8 +1454,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-Ra=\frac{\rho_{0}g_{0}\alpha_{0}\Delta TR_{0}^{3}}{\eta_{0}\kappa_{0}}\label{eq:Ra, Rayleigh number}\end{equation}
+\begin_inset Formula
+\begin{equation}
+Ra=\frac{\rho_{0}g_{0}\alpha_{0}\Delta TR_{0}^{3}}{\eta_{0}\kappa_{0}}\label{eq:Ra, Rayleigh number}
+\end{equation}
\end_inset
@@ -1434,8 +1501,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-Ra_{b}=Ra\frac{\delta\rho_{ph}}{\rho_{0}\alpha_{0}\Delta T}\label{eq:Rab, the phase-change Rayleigh number}\end{equation}
+\begin_inset Formula
+\begin{equation}
+Ra_{b}=Ra\frac{\delta\rho_{ph}}{\rho_{0}\alpha_{0}\Delta T}\label{eq:Rab, the phase-change Rayleigh number}
+\end{equation}
\end_inset
@@ -1444,8 +1513,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-Ra_{c}=Ra\frac{\delta\rho_{ch}}{\rho_{0}\alpha_{0}\Delta T}\label{eq:Rac, chemical Rayleigh number}\end{equation}
+\begin_inset Formula
+\begin{equation}
+Ra_{c}=Ra\frac{\delta\rho_{ch}}{\rho_{0}\alpha_{0}\Delta T}\label{eq:Rac, chemical Rayleigh number}
+\end{equation}
\end_inset
@@ -1454,8 +1525,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-Ra_{H}=RaH\frac{R_{0}^{3}-R_{CMB}^{3}}{3R_{0}^{3}}\label{eq:RaH, internal heating Rayleigh number}\end{equation}
+\begin_inset Formula
+\begin{equation}
+Ra_{H}=RaH\frac{R_{0}^{3}-R_{CMB}^{3}}{3R_{0}^{3}}\label{eq:RaH, internal heating Rayleigh number}
+\end{equation}
\end_inset
@@ -1463,8 +1536,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
-Di=\frac{\alpha_{0}g_{0}R_{0}}{c_{P0}}\label{eq:Di, dissipation number}\end{equation}
+\begin_inset Formula
+\begin{equation}
+Di=\frac{\alpha_{0}g_{0}R_{0}}{c_{P0}}\label{eq:Di, dissipation number}
+\end{equation}
\end_inset
@@ -1540,8 +1615,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\mathrm{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{u=0}}\label{eq:discrete continuite eqn}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\mathrm{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{u=0}}\label{eq:discrete continuite eqn}
+\end{equation}
\end_inset
@@ -1550,8 +1627,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\mathbf{A\mathit{u+}}\mathbf{B\mathit{p=f}}\label{eq:discrete momentum eqn}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\mathbf{A\mathit{u+}}\mathbf{B\mathit{p=f}}\label{eq:discrete momentum eqn}
+\end{equation}
\end_inset
@@ -1648,8 +1727,10 @@
\begin_layout Standard
\align right
-\begin_inset Formula \begin{equation}
-\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{f}}}\label{eq:cg}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{f}}}\label{eq:cg}
+\end{equation}
\end_inset
@@ -1711,8 +1792,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
-\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p^{(i)}=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{f-\mathbf{C}u^{(i-1)}}}}\label{eq:iter-cg}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p^{(i)}=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{f-\mathbf{C}u^{(i-1)}}}}\label{eq:iter-cg}
+\end{equation}
\end_inset
@@ -1740,8 +1823,10 @@
\end_inset
to eliminate the velocity unknowns:
-\begin_inset Formula \begin{equation}
-\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)A^{\mathit{-1}}\mathit{f}}}}\label{eq:bicg}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)A^{\mathit{-1}}\mathit{f}}}}\label{eq:bicg}
+\end{equation}
\end_inset
@@ -2107,8 +2192,8 @@
\end_layout
\begin_layout Itemize
-If using Pyre: Python 2.4 or greater, including header files (Python.h), and
- the pythia package (see below).
+If using Pyre: between Python 2.4 to 2.6, including header files (Python.h),
+ and the pythia package (see below).
\end_layout
\begin_layout Standard
@@ -2176,6 +2261,7 @@
CitcomSRegional
\family default
, and forgo use of Python and the Pyre framework.
+ By default in CitcomS 3.2.0 this is how CitcomS is configured.
This process requires only a C compiler and an MPI library.
For more information, see Section
\begin_inset CommandInset ref
@@ -2553,7 +2639,7 @@
\end_inset
.
-
+ Please note that Pyre in CitcomS does not work with Python 2.7 or higher.
\end_layout
\begin_layout Subsection
@@ -2596,7 +2682,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf CitcomS-3.1.0.tar.gz
+$ tar xzf CitcomS-3.2.0.tar.gz
\end_layout
\begin_layout Standard
@@ -2604,7 +2690,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c CitcomS-3.1.0.tar.gz | tar xf -
+$ gunzip -c CitcomS-3.2.0.tar.gz | tar xf -
\end_layout
\begin_layout Section
@@ -2630,7 +2716,7 @@
\begin_inset Newline newline
\end_inset
-$ cd CitcomS-3.1.0
+$ cd CitcomS-3.2.0
\end_layout
\begin_layout Enumerate
@@ -2893,7 +2979,7 @@
\end_layout
\begin_layout Standard
-The
+If Pyre is enabled, the
\family typewriter
configure
\family default
@@ -2977,7 +3063,7 @@
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="center" valignment="top" width="1in">
<column alignment="left" valignment="top" width="3.5in">
<row>
@@ -3511,7 +3597,7 @@
\end_layout
\begin_layout LyX-Code
-$ cd CitcomS-3.1.0/
+$ cd CitcomS-3.2.0/
\end_layout
\begin_layout LyX-Code
@@ -3911,30 +3997,45 @@
\end_inset
-Installing without Pyre
+Installing with Pyre
\end_layout
\begin_layout Standard
-To build CitcomS binaries just from the C code, give
+By default, CitcomS 3.2.0 does not install using Pyre.
+ To build CitcomS binaries with the Pyre wrappers (necessary for the example
+ Cookbooks), call
\family typewriter
configure
\family default
- the
+ using the
\family typewriter
---without-pyre
+--with-pyre
\family default
option:
\end_layout
\begin_layout LyX-Code
-$ ./configure --without-pyre
+$ ./configure --with-pyre=yes
\end_layout
\begin_layout Standard
The only system requirements for this configuration are an MPI library and
a C compiler.
- The
+ With Pyre the make command will build
\family typewriter
+pycitcoms
+\family default
+ and
+\family typewriter
+mpipycitcoms
+\family default
+ as well as the script
+\family typewriter
+citcoms
+\family default
+ used for running CitcomS.
+ Without Pyre the
+\family typewriter
make
\family default
command will build two command-line tools,
@@ -4057,8 +4158,8 @@
\end_inset
.
- The CitcomS v3.1.0 source package was created with Autoconf 2.61, Automake
- 1.9.6, and Libtool 1.5.26.
+ The CitcomS v3.2.0 source package was created with Autoconf 2.68, Automake
+ 1.11.2, and Libtool 2.4.2.
\end_layout
\begin_layout Subsection
@@ -6271,7 +6372,7 @@
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="0">
<column alignment="left" valignment="top" width="0">
<row>
@@ -6408,7 +6509,7 @@
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="16" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="0">
<column alignment="left" valignment="top" width="0">
<row>
@@ -8521,6 +8622,7 @@
\begin_layout Standard
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 from regional to full spherical shell problems
that address traditional mantle convection problems.
These cookbook examples are distributed with the package under the
@@ -9464,8 +9566,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
-visc=visc0\times exp\left(\frac{viscE+viscZ\times(1-r)}{T^{*}+viscT}-\frac{viscE+viscZ\times(1-r_{inner})}{1+viscT}\right)\label{eq:non-dim visc law}\end{equation}
+\begin_inset Formula
+\begin{equation}
+visc=visc0\times exp\left(\frac{viscE+viscZ\times(1-r)}{T^{*}+viscT}-\frac{viscE+viscZ\times(1-r_{inner})}{1+viscT}\right)\label{eq:non-dim visc law}
+\end{equation}
\end_inset
@@ -9497,9 +9601,11 @@
\end_inset
with the dimensional Arrhenius activation equation:
-\begin_inset Formula \begin{eqnarray}
+\begin_inset Formula
+\begin{eqnarray}
\eta & = & \eta_{0}exp\left(\frac{E_{a}+PV_{a}}{RT}\right)=\eta_{0}exp\left(\frac{E_{a}+PV_{a}}{R\Delta T\left(T'+T_{0}'\right)}\right)\nonumber \\
- & = & \eta_{0}exp\left(\frac{E_{a}+\rho g\left(1-r\right)V_{a}}{R\Delta T\left(T'+T_{0}'\right)}\right)=\eta_{0}exp\left(\frac{E_{a}/R\Delta T+\left(1-r\right)\rho gV_{a}/R\Delta T}{T'+T_{0}'}\right)\label{eq:arrhenius}\end{eqnarray}
+ & = & \eta_{0}exp\left(\frac{E_{a}+\rho g\left(1-r\right)V_{a}}{R\Delta T\left(T'+T_{0}'\right)}\right)=\eta_{0}exp\left(\frac{E_{a}/R\Delta T+\left(1-r\right)\rho gV_{a}/R\Delta T}{T'+T_{0}'}\right)\label{eq:arrhenius}
+\end{eqnarray}
\end_inset
@@ -9528,20 +9634,26 @@
\end_inset
, it is clear that
-\begin_inset Formula \begin{equation}
-viscE=\frac{E_{a}}{R\Delta T}\label{eq:viscE}\end{equation}
+\begin_inset Formula
+\begin{equation}
+viscE=\frac{E_{a}}{R\Delta T}\label{eq:viscE}
+\end{equation}
\end_inset
-\begin_inset Formula \begin{equation}
-viscZ=\frac{\rho gV_{a}}{R\Delta T}\label{eq:viscZ}\end{equation}
+\begin_inset Formula
+\begin{equation}
+viscZ=\frac{\rho gV_{a}}{R\Delta T}\label{eq:viscZ}
+\end{equation}
\end_inset
-\begin_inset Formula \begin{equation}
-viscT=T_{0}\label{eq:viscT}\end{equation}
+\begin_inset Formula
+\begin{equation}
+viscT=T_{0}\label{eq:viscT}
+\end{equation}
\end_inset
@@ -11652,8 +11764,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
-Nu_{surf}=H_{surf}\times(r_{outer}-r_{inner})\frac{r_{outer}}{r_{inner}}\label{eq:Nusselt number}\end{equation}
+\begin_inset Formula
+\begin{equation}
+Nu_{surf}=H_{surf}\times(r_{outer}-r_{inner})\frac{r_{outer}}{r_{inner}}\label{eq:Nusselt number}
+\end{equation}
\end_inset
@@ -11853,8 +11967,10 @@
\family default
specifies the nested levels of multigrid units and is subjected to the
following constraint:
-\begin_inset Formula \begin{equation}
-\mathrm{nodex}=1+\mathrm{nprocx}\times\mathrm{mgunitx}\times2^{levels-1}\label{eq:mgunit}\end{equation}
+\begin_inset Formula
+\begin{equation}
+\mathrm{nodex}=1+\mathrm{nprocx}\times\mathrm{mgunitx}\times2^{levels-1}\label{eq:mgunit}
+\end{equation}
\end_inset
@@ -11931,8 +12047,10 @@
The initial temperature is a conductive profile with a single spherical
harmonic perturbation.
The perturbation is located at mid-depth and is defined as:
-\begin_inset Formula \[
-mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)\]
+\begin_inset Formula
+\[
+mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)
+\]
\end_inset
@@ -13080,8 +13198,10 @@
\end_inset
can be rearranged according to Gauss's divergence theorem to become:
-\begin_inset Formula \begin{eqnarray}
-\ointop_{surface\ area}\rho_{0}\overrightarrow{u}\cdot\overrightarrow{n}dA & = & 0\label{eq:gauss div}\end{eqnarray}
+\begin_inset Formula
+\begin{eqnarray}
+\ointop_{surface\ area}\rho_{0}\overrightarrow{u}\cdot\overrightarrow{n}dA & = & 0\label{eq:gauss div}
+\end{eqnarray}
\end_inset
@@ -15186,7 +15306,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -15485,7 +15605,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="9" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -15823,7 +15943,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -16026,7 +16146,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -16217,7 +16337,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -16343,7 +16463,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -16460,7 +16580,7 @@
\align left
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
-<features islongtable="true">
+<features islongtable="true" longtabularalignment="center">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -16723,14 +16843,18 @@
\family default
in a comma-separated list.
The perturbation added to each layer is given by:
-\begin_inset Formula \[
-mag\times\cos(m\phi)\times P_{lm}(\cos\theta)\]
+\begin_inset Formula
+\[
+mag\times\cos(m\phi)\times P_{lm}(\cos\theta)
+\]
\end_inset
for the full sphere, and by:
-\begin_inset Formula \[
-mag\times\cos(\frac{\left(\theta-\theta_{min}\right)l\pi}{\theta_{max}-\theta_{min}})\times\cos(\frac{\left(\phi-\phi_{min}\right)m\pi}{\phi_{max}-\phi_{min}})\]
+\begin_inset Formula
+\[
+mag\times\cos(\frac{\left(\theta-\theta_{min}\right)l\pi}{\theta_{max}-\theta_{min}})\times\cos(\frac{\left(\phi-\phi_{min}\right)m\pi}{\phi_{max}-\phi_{min}})
+\]
\end_inset
@@ -16816,14 +16940,18 @@
3, the initial temperature is a conductive profile with perturbations to
all layers.
The perturbation is given by:
-\begin_inset Formula \[
-mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)\]
+\begin_inset Formula
+\[
+mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)
+\]
\end_inset
for the full sphere, and by:
-\begin_inset Formula \[
-mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\times\cos(\frac{\left(\theta-\theta_{min}\right)l\pi}{\theta_{max}-\theta_{min}})\times\cos(\frac{\left(\phi-\phi_{min}\right)m\pi}{\phi_{max}-\phi_{min}})\]
+\begin_inset Formula
+\[
+mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\times\cos(\frac{\left(\theta-\theta_{min}\right)l\pi}{\theta_{max}-\theta_{min}})\times\cos(\frac{\left(\phi-\phi_{min}\right)m\pi}{\phi_{max}-\phi_{min}})
+\]
\end_inset
@@ -16942,7 +17070,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -17221,7 +17349,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -17358,7 +17486,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="1" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -17426,7 +17554,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="20" columns="2">
-<features islongtable="true">
+<features islongtable="true" longtabularalignment="center">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -18340,7 +18468,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -18478,7 +18606,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="10" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -18881,7 +19009,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19075,7 +19203,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19163,7 +19291,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19279,7 +19407,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19420,7 +19548,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="10" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19795,7 +19923,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="1" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19867,7 +19995,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="1" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -19928,7 +20056,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -20121,7 +20249,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -20289,7 +20417,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -20378,7 +20506,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -20544,7 +20672,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -20616,7 +20744,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="23" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -21189,7 +21317,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="16" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -21578,7 +21706,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -21783,7 +21911,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="17" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -22195,7 +22323,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -22561,7 +22689,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -22881,7 +23009,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -23246,7 +23374,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -23588,7 +23716,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="13" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -23908,7 +24036,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="12" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -24205,7 +24333,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="15" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -24571,7 +24699,7 @@
\noindent
\begin_inset Tabular
<lyxtabular version="3" rows="31" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -25315,7 +25443,7 @@
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -25382,7 +25510,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -25522,7 +25650,7 @@
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -25750,7 +25878,7 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="1.85in">
<column alignment="left" valignment="top" width="4.25in">
<row>
@@ -26932,11 +27060,14 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \begin{equation}
+\begin_inset Formula
+\begin{equation}
\left[\begin{array}{ccc}
S_{\theta\theta} & S_{\theta\phi} & S_{\theta r}\\
S_{\phi\theta} & S_{\phi\phi} & S_{\phi r}\\
-S_{r\theta} & S_{r\phi} & S_{rr}\end{array}\right]\label{eq:symmetric stress tensor}\end{equation}
+S_{r\theta} & S_{r\phi} & S_{rr}
+\end{array}\right]\label{eq:symmetric stress tensor}
+\end{equation}
\end_inset
@@ -27022,7 +27153,7 @@
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="2">
-<features>
+<features tabularvalignment="middle">
<column alignment="center" valignment="top" width="0">
<column alignment="left" valignment="top" width="0">
<row>
@@ -27215,8 +27346,10 @@
\end_layout
\begin_layout Standard
-\begin_inset Formula \[
-{\displaystyle \sum}\left(S_{lm}\sin(m\phi)+C_{lm}\cos(m\phi)\right)P_{lm}(\cos\theta)\]
+\begin_inset Formula
+\[
+{\displaystyle \sum}\left(S_{lm}\sin(m\phi)+C_{lm}\cos(m\phi)\right)P_{lm}(\cos\theta)
+\]
\end_inset
Modified: doc/CitcomS/manual/citcoms.pdf
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Modified: doc/CitcomS/manual/graphics/citcoms_cover.pdf
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Modified: doc/CitcomS/manual/graphics/citcoms_cover.psd
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