[cig-commits] r4693 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Wed Oct 4 11:32:05 PDT 2006
Author: tan2
Date: 2006-10-04 11:32:04 -0700 (Wed, 04 Oct 2006)
New Revision: 4693
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Updated the Cookbook chapter
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-04 18:24:10 UTC (rev 4692)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-04 18:32:04 UTC (rev 4693)
@@ -2502,7 +2502,9 @@
\end_layout
\begin_layout Standard
-(TODO: precedence of various input methods)
+There are several methods to set the input parameters for CitComS.py, which
+ will be discussed in this section.
+
\end_layout
\begin_layout Subsection
@@ -2510,7 +2512,7 @@
\end_layout
\begin_layout Standard
-Pyre has the following syntax to change properties from their default values.
+Pyre has the following syntax to change properties from the command lines.
To change the value of a property of a component, use:
\end_layout
@@ -2571,6 +2573,15 @@
the syntax of it?)
\end_layout
+\begin_layout Subsection
+Precedences
+\end_layout
+
+\begin_layout Standard
+The command line input will override the input from the .cfg file, which
+ will in turn override the input from the .pml file.
+\end_layout
+
\begin_layout Section
Coordinate System and Mesh
\end_layout
@@ -2596,8 +2607,12 @@
fi
\emph default
are in units of radians.
- Figure 3.1(TODO: Sue, please please update '3.1' to an automatic tag) shows
- the organization of the mesh in a regional problem.
+ Figure
+\begin_inset LatexCommand \ref{fig:Global-Node-Numbering.}
+
+\end_inset
+
+ shows the organization of the mesh in a regional problem.
The numbering of the nodes is z-direction first, then x-direction, then
y-direction.
This numbering convention is used for the input and output data.
@@ -2613,6 +2628,8 @@
\begin_layout Description
\begin_inset Graphics
filename graphics/c_fig3.jpg
+ width 75page%
+ keepAspectRatio
\end_inset
@@ -2620,6 +2637,10 @@
\end_layout
\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Global-Node-Numbering.}
+
+\end_inset
+
Global Node Numbering.
Left: Global node numbering starts at the base of arrow A (theta
\size scriptsize
@@ -2680,8 +2701,11 @@
\end_layout
\begin_layout LyX-Code
-$ citcoms --steps=10 --controller.monitoringFrequency=5 --solver.datafile=example0
- --solver.mesher.nodex=17 --solver.mesher.nodey=17
+$ citcoms --steps=10 --controller.monitoringFrequency=5
+\backslash
+
+\newline
+--solver.datafile=example0 --solver.mesher.nodex=17 --solver.mesher.nodey=17
\end_layout
\begin_layout Standard
@@ -2870,6 +2894,33 @@
nprocy = 2
\end_layout
+\begin_layout Standard
+\begin_inset Float figure
+placement h
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename graphics/cookbook2.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Computational Domain.
+ Map view on the configuration of the top layer of the computational nodes
+ and the processors.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
File Systems and Output Formats
\end_layout
@@ -2972,7 +3023,11 @@
\family typewriter
example1.cfg
\family default
- --solver.datadir=/home/username --solver.output.output_format=ascii
+ --solver.datadir=/home/username
+\backslash
+
+\newline
+--solver.output.output_format=ascii
\end_layout
\begin_layout Standard
@@ -3029,7 +3084,11 @@
\family typewriter
example1.cfg
\family default
- --solver.datafile=/home/username/example1 --solver.output.output_format=hdf5
+ --solver.datafile=/home/username/example1
+\backslash
+
+\newline
+--solver.output.output_format=hdf5
\end_layout
\begin_layout Standard
@@ -3092,7 +3151,7 @@
\family typewriter
launcher.nodelist
\family default
- property is a comma-seperated list of machine names in square barckets.
+ property is a comma-seperated list of machine names in square brackets.
\end_layout
\begin_layout Standard
@@ -3102,7 +3161,7 @@
\family default
is generated.
It will contain a list of the nodes where CitComS.py has run.
- Save machine file as it will be useful in the post-processing step.
+ Save machine file as it will be useful in the postprocessing step.
\end_layout
\begin_layout Standard
@@ -3596,7 +3655,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\begin_inset Graphics
@@ -3749,10 +3808,6 @@
\end_layout
\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Global-Model-"Caps":}
-
-\end_inset
-
Global Model "Caps": Left (A): Three-dimensional perspective image showing
the 12 spherical caps used in a full CitComS.py run.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
@@ -3796,23 +3851,35 @@
\end_layout
\begin_layout Standard
-The last set of parameters includes the number of perturbations to the initial
- temperature (1), the number of nodal lines of the perturbation in the longitudi
-nal direction, e.g., spherical harmonic order (3), and the number of nodal
- lines in the latitudinal direction, e.g., spherical harmonic degree (2).
+The
+\family typewriter
+solver.ic
+\family default
+ facility control the temperature field for the initial conditions.
+ The last set of parameters includes the number of perturbations to the
+ initial temperature (1), the number of nodal lines of the perturbation
+ in the longitudinal direction, e.g., spherical harmonic order (3), the number
+ of nodal lines in the latitudinal direction, e.g., spherical harmonic degree
+ (2), which layer the pertubation is on (5), and the amplitude of the perturbati
+on (0.05).
Note that although the number of perturbations is assigned here as
\family typewriter
-solver.ic.num_perturbations=1
+num_perturbations=1
\family default
, that is actually the default value.
\end_layout
\begin_layout LyX-Code
-num_perturbations=1
+num_perturbations = 1
\newline
-perturbl=3
+perturbl = 3
\newline
-perturbm=2
+perturbm = 2
+\newline
+perturblayer = 5
+\newline
+perturbmag
+ = 0.05
\end_layout
\begin_layout Standard
@@ -3857,7 +3924,12 @@
\newline
perturbl = 3
\newline
-perturbm = 2
+perturbm = 2
+\newline
+perturblayer = 5
+\newline
+perturbmag
+ = 0.05
\end_layout
\begin_layout Standard
@@ -3927,8 +3999,11 @@
\end_layout
\begin_layout LyX-Code
-$ citcoms cookbook1.cfg --launcher.nodegen="n%03d" --launcher.nodelist=[1,1,1,1,1,1
-,1,1,1,1,1,1]
+$ citcoms cookbook1.cfg --launcher.nodegen="n%03d"
+\backslash
+
+\newline
+--launcher.nodelist=[1,1,1,1,1,1,1,1,1,1,1,1]
\end_layout
\begin_layout Standard
@@ -3951,13 +4026,8 @@
\begin_layout Standard
You would like to solve for thermal convection and with velocity boundary
conditions on the top surface within a given region of a sphere.
- You will need to modify a script that calls the regional version of CitComS,
+ You will need to use the regional version of CitComS.py.
-\family typewriter
-citcomsregional.sh
-\family default
-.
-
\end_layout
\begin_layout Subsection
@@ -3965,83 +4035,33 @@
\end_layout
\begin_layout Standard
-You will be running
+You will be using
\family typewriter
-cookbook2.sh
+cookbook2.cfg
\family default
-, which calls the script
-\family typewriter
-citcomsregional.sh
-\family default
.
- The parameters specify the number of processors or nodes (4), time steps
- (61), the location of the output (
+ The parameters specify the number of time steps (61), the prefix of the
+ output filenames (
\family typewriter
-/scratch/username/cookbook2
+cookbook2
\family default
), and how often the computation will be monitored (30).
\end_layout
\begin_layout LyX-Code
---steps=61
-\backslash
-
+steps = 61
+\newline
+monitoringFrequency = 30
+\newline
+datafile = cookbook2
\end_layout
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---controller.monitoringFrequency=30
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodes=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[101-102,101-102]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile=/scratch/username/cookbook2
-\backslash
-
-\end_layout
-
\begin_layout Standard
The
\family typewriter
solver.mesher
\family default
- has several properties involved in the generation of the computational
+ facility has several properties involved in the generation of the computational
mesh.
Continue to use the default values for the physical portion of the domain
in which you are interested.
@@ -4050,63 +4070,18 @@
\end_layout
\begin_layout LyX-Code
---solver.mesher.nprocx=2
-\backslash
-
+nprocx = 2
+\newline
+nprocy = 2
+\newline
+nodex = 17
+\newline
+nodey = 17
+\newline
+nodez = 9
\end_layout
-\begin_layout LyX-Code
---solver.mesher.nprocy=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodex=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodey=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodez=9
-\backslash
-
-\end_layout
-
\begin_layout Standard
-\begin_inset Float figure
-placement h
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\begin_inset Graphics
- filename graphics/cookbook2.eps
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Caption
-Computational View.
- Top view configuration of the layer of the computational nodes and the
- processors.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
The
\family typewriter
solver.bc
@@ -4118,8 +4093,19 @@
\end_inset
-).In addition, the initial temperature field has a linear conductive profile.
- The amplitude of horizontal temperature perturbation is set to zero using
+ for how to dimensionalize it).
+
+\end_layout
+
+\begin_layout LyX-Code
+topvbc = 1
+\newline
+topvbxval = 100
+\end_layout
+
+\begin_layout Standard
+In addition, the initial temperature field has a linear conductive profile.
+ The amplitude of initial temperature perturbation is set to zero using
the
\family typewriter
solver.ic
@@ -4128,54 +4114,139 @@
\end_layout
-\begin_layout Standard
-
-\end_layout
-
\begin_layout LyX-Code
---solver.bc.topvbc=1
-\backslash
-
+num_perturbations = 1
+\newline
+perturbmag = 0.0
\end_layout
-\begin_layout LyX-Code
---solver.bc.topvbxval=100
-\backslash
-
+\begin_layout Paragraph
+Example: Velocity Boundary Conditions, cookbook2.cfg
\end_layout
\begin_layout LyX-Code
---solver.bc.topvbyval=0
-\backslash
+[CitcomS]
+\newline
+steps = 61 ; number of time steps
+\newline
-\end_layout
+\newline
+[CitcomS.controller]
+\newline
+mo
+nitoringFrequency = 30 ; how often to monitor the computation
+\newline
-\begin_layout LyX-Code
+\newline
+[CitcomS.solver]
+\newline
+d
+atafile = cookbook2 ; prefix of output filenames
+\newline
-\backslash
-
-\end_layout
+\newline
+# Modify the layout
+ of the mesh.
+\newline
+[CitcomS.solver.mesher]
+\newline
+nprocx = 2
+\newline
+nprocy = 2
+\newline
+nodex = 17
+\newline
+nodey
+ = 17
+\newline
+nodez = 9
+\newline
-\begin_layout LyX-Code
---solver.ic.num_perturbations=1
-\backslash
+\newline
+# Impose a uniform velocity across the top surface.
+\newline
+[CitcomS.solve
+r.bc]
+\newline
+topvbc = 1
+\newline
+topvbxval = 100
+\newline
-\end_layout
+\newline
+# Modify the layout of the mesh.
+\newline
+[CitcomS.solver.m
+esher]
+\newline
+nprocx = 2
+\newline
+nprocy = 2
+\newline
+nodex = 17
+\newline
+nodey = 17
+\newline
+nodez = 9
+\newline
-\begin_layout LyX-Code
---solver.ic.perturbmag=0.0
+\newline
+# Impose a
+ uniform velocity across the top surface.
+\newline
+[CitcomS.solver.bc]
+\newline
+topvbc = 1
+\newline
+topvbxva
+l = 100
+\newline
+topvbyval = 0
+\newline
+
+\newline
+# In addition, to determine the temperature, the temperatu
+re field
+\newline
+# associated only with this imposed velocity, reset the initial
+\newline
+#
+ perturbation to zero.
+\newline
+[CitcomS.solver.ic]
+\newline
+num_perturbations = 1
+\newline
+perturbmag
+ = 0.0
\end_layout
\begin_layout Subsection
-Cookbook 2: Velocity Boundary Conditions
+Discussion
\end_layout
\begin_layout Standard
+Using OpenDX to visualize the results (Figure
+\begin_inset LatexCommand \ref{fig:Cookbook-2:-Velocity}
+
+\end_inset
+
+), this model allows you to create a plate-driven convection in which there
+ is a thermal upwelling on one wall, a thermal downwelling on another, and
+ uniform horizontal velocity across the top.
+ The downwelling is not exactly subduction because the default boundary
+ conditions are close to zero shear stress on the boundaries.
+ This means that there is a symmetrical downwelling in a vertical domain
+ on the other side.
+
+\end_layout
+
+\begin_layout Standard
\begin_inset Float figure
placement h
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\begin_inset Graphics
@@ -4191,12 +4262,7 @@
\end_inset
-\InsetSpace ~
-Cookbook\InsetSpace ~
-2: \InsetSpace ~
-Velocity\InsetSpace ~
-Boundary\InsetSpace ~
-Conditions.
+Cookbook 2: Velocity Boundary Conditions.
This model highlights a region of the sphere and the heated upwellings
(warm colors), downwellings (cool colors), and the velocities (yellow arrows).
\end_layout
@@ -4206,172 +4272,6 @@
\end_layout
-\begin_layout LyX-Code
-#!/bin/sh
-\newline
-
-\newline
-../../tests/citcomsregional.sh
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---steps=61
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---controller.monitoringFrequency=30
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodes=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[101-102,101-102]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile=cookbook2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocx=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocy=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodex=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodey=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodez=9
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.topvbc=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.topvbxval=100
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.topvbyval=0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.num_perturbations=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbmag=0.0
-\end_layout
-
-\begin_layout Subsection
-Discussion
-\end_layout
-
-\begin_layout Standard
-Using OpenDX to visualize the results (Figure
-\begin_inset LatexCommand \ref{fig:Cookbook-2:-Velocity}
-
-\end_inset
-
-), this model allows you to create a plate-driven convection in which there
- is a thermal upwelling on one wall, a thermal downwelling on another, and
- uniform horizontal velocity across the top.
- The downwelling is not exactly subduction because the default boundary
- conditions are close to zero shear stress on the boundaries.
- This means that there is a symmetrical downwelling in a vertical domain
- on the other side.
-
-\end_layout
-
\begin_layout Section
Cookbook 3: Temperature-Dependent Viscosity
\end_layout
@@ -4391,327 +4291,186 @@
\end_layout
\begin_layout Standard
-You will be running
+You will be using cookbook3.cfg.
+ The parameters specify the number of time steps (200), how often the computatio
+n will be monitored (25), the prefix of the output filenames (
\family typewriter
-cookbook3.sh
+cookbook3
\family default
-, which calls the script
-\family typewriter
-citcomsregional.sh
-\family default
-.
- The parameters specify the number of processors (4) and their names, time
- steps (200), the location of the output (
-\family typewriter
-/scratch/username/cookbook3
-\family default
-) and how often the computation will be monitored (25).
-\end_layout
+), and the Rayleigh number (
+\begin_inset Formula $10^{\text{6}}$
+\end_inset
-\begin_layout LyX-Code
---steps=200
-\backslash
-
+).
\end_layout
\begin_layout LyX-Code
-
-\backslash
-
+steps = 200
+\newline
+monitoringFrequency = 25
+\newline
+datafile = cookbook3
+\newline
+rayleigh = 1e6
\end_layout
-\begin_layout LyX-Code
---controller.monitoringFrequency=25
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodes=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[101-102,101-102]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile=cookbook3
-\backslash
-
-\end_layout
-
\begin_layout Standard
The
\family typewriter
-solver.rayleigh
+solver.visc
\family default
- indicates the Rayleigh number you would like to set and the
+ facility assign the viscosities.
+ The parameters specify whether the viscosity should be updated at every
+ time step (
\family typewriter
-solver.visc
+on
\family default
- parameters assign the viscosities.
-\end_layout
-
-\begin_layout LyX-Code
---solver.rayleigh=1e6
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VISC_UPDATE=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.num_mat=4
-\backslash
+), the number of viscous layers (4), the viscosity of each layer (1,1,1,1),
+ whether the viscosity is temperature dependent (
+\family typewriter
+on
+\family default
+), the activation energy of each layer (0.2,0.2,0.2,0.2), the temperature offset
+ of each layer (0,0,0,0), whether to apply the minimum cutoff (
+\family typewriter
+on
+\family default
+), the value of the minimum cutoff (1.0), whether to apply the maximum cutoff
+ (
+\family typewriter
+on
+\family default
+), at the value of the maximum cutoff (100.0).
\end_layout
\begin_layout LyX-Code
---solver.visc.visc0=1,1,1,1
-\backslash
-
+VISC_UPDATE = on
+\newline
+num_mat = 4
+\newline
+visc0 = 1,1,1,1
+\newline
+TDEPV = on
+\newline
+viscE = 0.2,0.2,0.2,0.2
+\newline
+viscT
+ = 0,0,0,0
+\newline
+VMIN = on
+\newline
+visc_min = 1.0
+\newline
+VMAX = on
+\newline
+visc_max = 100.0
\end_layout
-\begin_layout LyX-Code
---solver.visc.TDEPV=on
-\backslash
-
+\begin_layout Standard
+The range of the layers are determined by the following parameters: layer
+ 1 extends from the top surface to a depth of
+\family typewriter
+solver.const.z_lith
+\family default
+ (default to 0.014, or 90 km dimensionally); layer 2 is below layer 1 and
+ extends to a depth of
+\family typewriter
+solver.const.z_410
+\family default
+ (default to 0.06435, or 410 km dimensionally); ayer 3 is below layer 2 and
+ extends to a depth of
+\family typewriter
+solver.const.z_lmantle
+\family default
+ (default to 0.105, or 670 km dimensionally); layer 4 is below layer 3 and
+ extends to the bottom.
+ The temperature dependence of the viscosity of each layer is determined
+ by: (TODO: equation # is not right...)
\end_layout
-\begin_layout LyX-Code
---solver.visc.viscE=0.2,0.2,0.2,0.2
-\backslash
+\begin_layout Standard
+\align right
+\begin_inset Formula \begin{equation}
+visc=visc0*exp\left(\frac{viscE}{T+viscT}-\frac{viscE}{1+viscT}\right)\label{eq:17}\end{equation}
-\end_layout
+\end_inset
-\begin_layout LyX-Code
---solver.visc.viscT=0,0,0,0
-\backslash
-
-\end_layout
-\begin_layout LyX-Code
---solver.visc.VMIN=on
-\backslash
-
\end_layout
-\begin_layout LyX-Code
---solver.visc.visc_min=1.0
-\backslash
-
+\begin_layout Paragraph
+Example: Temperature-Dependent Viscosity, cookbook3.cfg
\end_layout
\begin_layout LyX-Code
---solver.visc.VMAX=on
-\backslash
-
-\end_layout
+[CitcomS]
+\newline
+steps = 200 ; number of time steps
+\newline
-\begin_layout LyX-Code
---solver.visc.visc_max=100.0
-\end_layout
+\newline
+[CitcomS.controller]
+\newline
+mo
+nitoringFrequency = 25 ; how often to monitor the computation
+\newline
-\begin_layout Subsection
-Cookbook 3: Temperature-Dependent Viscosity
-\end_layout
+\newline
+[CitcomS.solver]
+\newline
+d
+atafile = cookbook3 ; prefix of output filenames
+\newline
+rayleigh = 1e6
+ ; Rayleigh number
+\newline
-\begin_layout LyX-Code
-#!/bin/sh
\newline
+# Modify the layout of the mesh.
+\newline
+[CitcomS.solver.mesher
+]
+\newline
+nprocx = 2
+\newline
+nprocy = 2
+\newline
+nodex = 17
+\newline
+nodey = 17
+\newline
+nodez = 9
+\newline
\newline
-../../tests/citcomsregional.sh
-\backslash
+# Assign the viscosities.
+\newline
+[CitcomS.solver.visc]
+\newline
+VISC_UPDATE = on
+\newline
+num_mat = 4
+\newline
+visc0 = 1,1,1,1
+\newline
+TDEPV = on
+\newline
+viscE
+ = 0.2,0.2,0.2,0.2
+\newline
+viscT = 0,0,0,0
+\newline
+VMIN = on
+\newline
+visc_min = 1.0
+\newline
+VMAX = on
+\newline
+visc_max = 100.0
\end_layout
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---steps=200
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---controller.monitoringFrequency=25
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodes=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[101-102,101-102]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.rayleigh=1e6
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile=cookbook3
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocx=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocy=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodex=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodey=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodez=9
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VISC_UPDATE=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.num_mat=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc0=1,1,1,1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.TDEPV=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.viscE=0.2,0.2,0.2,0.2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.viscT=0,0,0,0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VMIN=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc_min=1.0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VMAX=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc_max=100.0
-\end_layout
-
\begin_layout Standard
\begin_inset Float figure
placement H
@@ -4729,10 +4488,7 @@
\end_layout
\begin_layout Caption
-Cookbook\InsetSpace ~
-3:\InsetSpace ~
-Temperature-Dependent\InsetSpace ~
-Viscosity.
+Cookbook 3: Temperature-Dependent Viscosity.
This model highlights a region that features both the heated upwelling
(warm colors) and the even distribution of the velocities (arrows).
\end_layout
@@ -4767,371 +4523,171 @@
\begin_layout Standard
The parameter that controls if a mesh is to be uniform or refined is
\family typewriter
-coor
+solver.mesher.coor
\family default
.
- Set the
+ Set it to
\family typewriter
-coor
-\family default
- to
-\family typewriter
on (solver.mesher.coor=on)
\family default
- in order to read the uneven mesh point coordinates from an input file (such
- as
+ in order to read the uneven mesh point coordinates from an input file (specifie
+d by
\family typewriter
-coor.dat
-\family default
-).
- The format of the coordinate input file,
-\family typewriter
coor_file
\family default
-, is described in Appendix
-\begin_inset LatexCommand \ref{sec:Coordinate-files}
+).
+ The format of the coordinate input file is described in Appendix
+\begin_inset LatexCommand \vref{sec:Coordinate-files}
\end_inset
.
\end_layout
-\begin_layout Subsection
-Cookbook 4: Regionally Refined Meshes Coordinate File Example
-\end_layout
-
\begin_layout LyX-Code
-nsd=1
-\backslash
-
+coor = on
+\newline
+coor_file = coor.dat
\end_layout
-\begin_layout LyX-Code
-theta_min
-\backslash
-
+\begin_layout Standard
+The computational domain is bounded in colatitude between radian 1 and 2,
+ in latitude between radian 0 and 1, and in radius between 0.55 and 1.
\end_layout
\begin_layout LyX-Code
-theta_max
-\backslash
-
+theta_min = 1
+\newline
+theta_max = 2
+\newline
+fi_min = 0
+\newline
+fi_max = 1
+\newline
+radius_inner = 0.55
+\newline
+radius_outer
+ = 1
\end_layout
-\begin_layout LyX-Code
-
-\backslash
-
+\begin_layout Paragraph
+Example: Regionally Refined Meshes, cookbook4.cfg
\end_layout
\begin_layout LyX-Code
-nsd=2
-\backslash
-
-\end_layout
+[CitcomS]
+\newline
+steps = 250 ; number of time steps
+\newline
-\begin_layout LyX-Code
-fi_min
-\backslash
-
-\end_layout
+\newline
-\begin_layout LyX-Code
-fi_max
-\backslash
-
-\end_layout
+\newline
+[CitcomS.controller]
+\newline
+mo
+nitoringFrequency = 10 ; how often to monitor the computation
+\newline
-\begin_layout LyX-Code
+\newline
-\backslash
-
-\end_layout
+\newline
+[CitcomS.solver]
+\newline
+r
+ayleigh = 1e6 ; Rayleigh number
+\newline
+datafile = cookbook4
+ ; prefix of output filenames
+\newline
-\begin_layout LyX-Code
-nsd=3
-\backslash
+\newline
-\end_layout
+\newline
+[CitcomS.solver.ic]
+\newline
+num_perturbations = 1
+\newline
+perturbmag
+ = 0.05
+\newline
+perturblayer = 10
+\newline
-\begin_layout LyX-Code
-radius_inner
-\backslash
-
-\end_layout
+\newline
+# Perturb the initial temperature gradient in the
+ longitudinal
+\newline
+# direction.
+\newline
+perturbl = 1
+\newline
+perturbm = 0
+\newline
-\begin_layout LyX-Code
-radius_outer
-\backslash
-
-\end_layout
+\newline
-\begin_layout Subsection
-Cookbook 4: Regionally Refined Meshes
-\end_layout
-
-\begin_layout LyX-Code
-#!/bin/sh
\newline
+[CitcomS.solver.mesher]
+\newline
+# Read
+ uneven mesh point coordinates from 'coor.dat'.
+\newline
+coor = on
+\newline
+coor_file = coor.dat
+\newline
+nprocx
+ = 4
+\newline
+nprocy = 2
+\newline
+nprocz = 2
+\newline
+nodex = 33
+\newline
+nodey = 17
+\newline
+nodez = 17
+\newline
+theta_min = 1
+\newline
+theta_max
+ = 2
+\newline
+fi_min = 0
+\newline
+fi_max = 1
+\newline
\newline
-../../tests/citcomsregional.sh
-\backslash
+\newline
+[CitcomS.solver.visc]
+\newline
+VISC_UPDATE = on
+\newline
+num_mat = 4
+\newline
+visc0
+ = 1,1,1,1
+\newline
+TDEPV = on
+\newline
+viscE = 0.2,0.2,0.2,0.2
+\newline
+viscT = 0,0,0,0
+\newline
+VMIN = on
+\newline
+visc_min
+ = 1.0
+\newline
+VMAX = on
+\newline
+visc_max = 100.0
\end_layout
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---steps=250
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---controller.monitoringFrequency=10
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodes=32
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[151-166,151-166]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.rayleigh=1e6
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile=cookbook4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.num_perturbations=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbmag=0.05
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbl=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbm=0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturblayer=10
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.coor=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.coor_file=/scratch/username/coor.dat
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocx=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocy=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocz=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodex=33
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodey=33
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodez=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.levels=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.theta_min=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.theta_max=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.fi_min=0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.fi_max=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VISC_UPDATE=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.num_mat=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc0=1,1,1,1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.TDEPV=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.viscE=0.2,0.2,0.2,0.2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.viscT=0,0,0,0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VMIN=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc_min=1.0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VMAX=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc_max=100.0
-\backslash
-
-\end_layout
-
\begin_layout Standard
\begin_inset Float figure
placement H
@@ -5149,13 +4705,9 @@
\end_layout
\begin_layout Caption
-Cookbook\InsetSpace ~
-4:\InsetSpace ~
-Regionally\InsetSpace ~
-Refined\InsetSpace ~
-Mesher: This model shows the temperature (upwelling
- -- warm colors, downwelling -- cool colors) and the uneven distribution
- of the velocities (yellow arrows).
+Cookbook 4: Regionally Refined Mesher: This model shows the temperature
+ (upwelling -- warm colors, downwelling -- cool colors) and the uneven distribut
+ion of the velocities (yellow arrows).
Note the refined mesh for the left and bottom regions of the model (inset).
\end_layout
@@ -5223,45 +4775,33 @@
Initially, both plates have Euler poles situated far apart, so the velocities
are approximately constants (about 5 cm/yr for the left plate and about
2 cm/yr for the right plate).
- After 30 Ma a pole jump occurred for the right slab only, so the Euler
+ After 30 Ma, a pole jump occurred for the right slab only, so the Euler
pole moved closer.
- Since we impose a top velocity boundary in our model, the following parameters
- should be turned on:
+
\end_layout
\begin_layout Standard
-
+Since we impose a top velocity boundary in our model, the following parameters
+ should be turned on:
\end_layout
\begin_layout LyX-Code
---solver.bc.topvbc=1
-\backslash
-
+topvbc = 1
+\newline
+file_vbcs = on
\end_layout
-\begin_layout LyX-Code
---solver.param.file_vbcs=on
-\backslash
-
-\end_layout
-
\begin_layout Standard
The following two lines specify the location of the velocity files and the
starting age for the model:
\end_layout
\begin_layout LyX-Code
---solver.param.vel_bound_file=$PWD/velocity/vel.dat
-\backslash
-
+start_age = 55
+\newline
+vel_bound_file = ./velocity/bvel.dat
\end_layout
-\begin_layout LyX-Code
---solver.param.start_age=55
-\backslash
-
-\end_layout
-
\begin_layout Standard
Since the starting age is set to 55 Ma, there will be 57 velocity files,
one for each Ma (
@@ -5269,376 +4809,54 @@
vel.dat0, vel.dat1,...vel.dat55, vel.dat56
\family default
).
- The format of the velocity file is a two-column ASCII file, formatted as
- follows:
-\end_layout
+ The format of the velocity file is described in Appendix
+\begin_inset LatexCommand \vref{sec:Velocity-boundary-condition}
-\begin_layout LyX-Code
-v_theta v_fi
-\end_layout
+\end_inset
-\begin_layout LyX-Code
-......
+.
\end_layout
\begin_layout Standard
-There will be as many lines as the total number of nodes for the top plane
- (
+When
\family typewriter
-nodex*nodey
+restart=on
\family default
-).
-
-\end_layout
+ is set, the initial temperature field is read from files.
+ The files have the same naming scheme and format as the CitComS velo output,
+ as described in Appendix
+\begin_inset LatexCommand \vref{sub:Velocity-and-Temperature}
-\begin_layout Subsection
-Cookbook 5: Subduction Models with Trench Rollback
+\end_inset
+
+.
+ The prefix of the filename is specified in
+\family typewriter
+datafile_old
+\family default
+, and the time step of the velo file in
+\family typewriter
+solition_cycles_init
+\family default
+.
+ In this example, a processor of MPI rank
+\family typewriter
+n
+\family default
+ will read file
+\family typewriter
+./restart_files/cookbook5.velo.n.0
\end_layout
\begin_layout LyX-Code
-#!/bin/sh
+datafile_old = ./restart_files/cookbook5
\newline
-
+restart = on
\newline
-../../tests/citcomsregional.sh
-\backslash
-
+solution_cycles_init
+ = 0
\end_layout
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---steps=1000
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---controller.monitoringFrequency=10
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodes=64
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[131-162]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile=cookbook5
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.rayleigh=4.07e+08
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.topvbc=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.param.file_vbcs=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.param.vel_bound_file=$PWD/velocity/bvel.dat
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.param.start_age=55
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.restart=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.solution_cycles_init=0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile_old=$PWD/restart_files/cookbook5
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.temperature_bound_adj=off
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.depth_bound_adj=0.157000
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.bc.width_bound_adj=0.050000
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.coor=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.coor_file=$PWD/coor.dat
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.mgunitx=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocx=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocy=8
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nprocz=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodex=17
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodey=65
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.nodez=33
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.levels=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.theta_min=1.47
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.theta_max=1.67
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.fi_min=0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.fi_max=0.5
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.mesher.radius_inner=0.7
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VISC_UPDATE=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.rheol=3
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.const.refvisc=4e+21
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.num_mat=4
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc0=100,0.003,1,2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.TDEPV=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.viscE=24,24,24,24
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.viscT=0.182,0.182,0.182,0.182
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VMIN=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc_min=0.01
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.VMAX=on
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.visc.visc_max=100.0
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-# End of file
-\end_layout
-
\begin_layout Standard
\begin_inset Float figure
placement H
@@ -5662,9 +4880,7 @@
\end_inset
-\InsetSpace ~
-Cookbook\InsetSpace ~
-5: Left (A): initially, both plates have Euler poles (magenta and
+Cookbook 5: Left (A): initially, both plates have Euler poles (magenta and
green dots) situated far apart from the plate, so the velocities are approximat
e constants (about 5 cm/yr for the left plate and about 2 cm/yr for the
right plate).
@@ -5677,6 +4893,125 @@
\end_layout
+\begin_layout Paragraph
+Example: Subduction Models with Trench Rollback, cookbook5.cfg
+\end_layout
+
+\begin_layout LyX-Code
+[CitcomS]
+\newline
+steps = 1000 ; number of time steps
+\newline
+
+\newline
+[CitcomS.controller]
+\newline
+mo
+nitoringFrequency = 10 ; how often to monitor the computation
+\newline
+
+\newline
+[CitcomS.solver]
+\newline
+d
+atafile = cookbook5
+\newline
+datafile_old = ./restart_files/cookbook5
+\newline
+rayleigh = 4.07e+08
+\newline
+
+\newline
+[Cit
+comS.solver.bc]
+\newline
+topvbc = 1
+\newline
+
+\newline
+[CitcomS.solver.param]
+\newline
+file_vbcs = on
+\newline
+start_age = 55
+\newline
+
+\newline
+#
+ Since the starting age is set to 55 Ma, there will be 56 velocity
+\newline
+# files,
+ one for each Ma (bvel.dat0, bvel.dat1, ...
+ bvel.dat56).
+\newline
+vel_bound_file = ./velocity/bvel.dat
+\newline
+
+\newline
+[CitcomS.solver.ic]
+\newline
+restart =
+ on
+\newline
+solution_cycles_init = 0
+\newline
+
+\newline
+[CitcomS.solver.mesher]
+\newline
+coor = on
+\newline
+coor_file = ./coor.dat
+\newline
+npr
+ocx = 2
+\newline
+nprocy = 8
+\newline
+nprocz = 4
+\newline
+nodex = 17
+\newline
+nodey = 65
+\newline
+nodez = 33
+\newline
+theta_min = 1.47
+\newline
+theta_ma
+x = 1.67
+\newline
+fi_min = 0
+\newline
+fi_max = 0.5
+\newline
+radius_inner = 0.7
+\newline
+
+\newline
+[CitcomS.solver.visc]
+\newline
+num_mat
+ = 4
+\newline
+visc0 = 100,0.003,1,2
+\newline
+TDEPV = on
+\newline
+viscE = 24,24,24,24
+\newline
+viscT = 0.182,0.182,0.182,0.182
+\newline
+
+VMIN = on
+\newline
+visc_min = 0.01
+\newline
+VMAX = on
+\newline
+visc_max = 100.0
+\end_layout
+
\begin_layout Standard
\begin_inset Float figure
placement h
@@ -5698,9 +5033,7 @@
\end_inset
-\InsetSpace ~
-Cookbook\InsetSpace ~
-5: The pole jump after 30 Ma produced a flat slab on one side (fore
+Cookbook 5: The pole jump after 30 Ma produced a flat slab on one side (fore
side) and a steep slab on the other side (back side).
\end_layout
@@ -5731,7 +5064,7 @@
\end_layout
\begin_layout Section
-Cookbook 6: Pseudo-free-surface Formulation
+Cookbook 6: Pseudo-Free-Surface Formulation
\end_layout
\begin_layout Subsection
@@ -5748,7 +5081,7 @@
to short wavelength topography is of interest or the lithosphere has a
very high effective viscosity.
Another situation where free-surface formulation is desired is when two
- Pyre solvers, Snac and CitCom, are coupled.
+ Pyre solvers, Snac and CitCom.py, are coupled.
\end_layout
\begin_layout Standard
@@ -5788,22 +5121,18 @@
\end_layout
\begin_layout Standard
-To verify that the above algorithm works, you will run two different CitCom-only
+To verify that the above algorithm works, you will run two different CitComS.py
models with each BC (free-slip and pseudo-free-surface) and compare the
topography computed accordingly.
The scripts
\family typewriter
-citcom_only_freeslip.sh
+cookbook6.cfg
\family default
-,
-\family typewriter
-citcom_only_freesurf.sh
-\family default
will include the following parameters.
\end_layout
\begin_layout Itemize
-Domain size: 45 deg x 45 deg x 1200 km
+Domain size: 45 deg x 45 deg x 1200 km
\end_layout
\begin_layout Itemize
@@ -5825,25 +5154,17 @@
\end_layout
\begin_layout Itemize
-solver.tsolver.fixed_timestep=7.770000e-10 (= ~1000 yrs)
-\end_layout
-\begin_layout Itemize
-solver.bc.pseudo_free_surf=on/off
+\family typewriter
+solver.tsolver.fixed_timestep=7.770000e-10
+\family default
+ (= ~1000 yrs)
\end_layout
\begin_layout Itemize
-scripts for running test models:
-\end_layout
-\begin_layout LyX-Code
-
\family typewriter
-citcom_only_freeslip.sh
-\family default
-,
-\family typewriter
-citcom_only_freesurf.sh
+solver.bc.pseudo_free_surf=on
\end_layout
\begin_layout Subsection
@@ -5863,15 +5184,6 @@
\end_layout
-\begin_layout Quote
-
-\series bold
-Note:
-\series default
- the unit of x axis is radians, not degrees.
-
-\end_layout
-
\begin_layout Standard
\begin_inset Float figure
placement h
@@ -5891,6 +5203,7 @@
\begin_layout Caption
Cookbook 6.
Graphs of topography profiles.
+ The unit of x axis is radians, not degrees.
\end_layout
@@ -5918,7 +5231,7 @@
\begin_layout Standard
Most of the properties have identical names for the parameters as those
- used in the regular version of CitComS.
+ used in the none-pyre version of CitComS.
This section highlights those which have changed and those which are entirely
new.
All the parameters which can be set are included in an appendix at the
@@ -7760,14 +7073,18 @@
\family default
\size default
controls how CitComS.py, an MPI application, is executed on multiple processors.
- It is the equivalent to mpirun in MPICH.
+ It is the equivalent to
+\family typewriter
+mpirun
+\family default
+ in MPI.
\end_layout
\begin_layout Standard
\noindent
\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="2">
+<lyxtabular version="3" rows="4" columns="2">
<features islongtable="true">
<column alignment="left" valignment="top" leftline="true" width="1.75in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
@@ -7809,11 +7126,7 @@
list of machine names.
Example:
\family typewriter
-n%
-\begin_inset Formula $\textrm{\O}$
-\end_inset
-
-3d
+n%03d
\end_layout
\end_inset
@@ -7842,26 +7155,6 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-nodes
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Number of machine nodes.
-\end_layout
-
-\end_inset
-</cell>
-</row>
<row topline="true" bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
@@ -10928,7 +10221,7 @@
\end_layout
\begin_layout Chapter
-CitComS Input File Format
+CitComS.py Input File Format
\end_layout
\begin_layout Section*
@@ -10936,7 +10229,7 @@
\end_layout
\begin_layout Standard
-CitComS expects Unix-styled ASCII files (i.e., no carriage character following
+CitComS.py expects Unix-styled ASCII files (i.e., no carriage character following
new line character) for all input files.
This can be a nuisance in DOS/Windows systems.
You may want to find a text editor that can write Unix-style ASCII files.
@@ -10962,11 +10255,11 @@
\end_layout
\begin_layout Standard
-For
+For regional version of
\family typewriter
-regCitComS
+CitComS
\family default
-, the mesh must be regular, but the mesh spacing may be unequal.
+.py, the mesh must be regular, but the mesh spacing may be unequal.
The
\family typewriter
coor_file
@@ -11073,11 +10366,12 @@
\end_layout
\begin_layout Standard
-For
+For full spherical version of
\family typewriter
-fullCitComS
+CitComS
\family default
-, the mesh must be regular and equidistant in the horizontal dimension.
+.py, the mesh of each cap must be regular and equidistant in the horizontal
+ dimension.
Only vertical dimension is specified by
\family typewriter
coor_file
@@ -11123,6 +10417,10 @@
\end_layout
\begin_layout Section*
+\begin_inset LatexCommand \label{sec:Velocity-boundary-condition}
+
+\end_inset
+
Velocity boundary condition files
\end_layout
@@ -11325,21 +10623,28 @@
\end_layout
\begin_layout Standard
-In this version of CitComS, the implementation of tracer is neither parallelized
-, nor has it been tested.
+In this version of CitComS.py, the implementation of tracer is neither paralleliz
+ed, nor has it been tested.
We strongly advise you not to use this feature.
The format of
\family typewriter
tracer_file
\family default
- is described here for completion:
+ is described here for completion.
+ The first line is the number of tracers in the file.
+ The rest is the location of the tracers.
+
\end_layout
\begin_layout LyX-Code
+
+\series bold
num_tracers
\end_layout
\begin_layout LyX-Code
+
+\series bold
type x y z
\end_layout
@@ -11348,7 +10653,7 @@
\end_inset
-CitComS Output File Format
+CitComS.py Output File Format
\end_layout
\begin_layout Section*
@@ -11368,14 +10673,10 @@
\family typewriter
autocombine.py
\family default
- and
-\family typewriter
-batchcombine.py
-\family default
- produce 1 cap file for regional CitComS and 12 cap files for full CitComS,
+ produce 1 cap file for regional CitComS.py and 12 cap files for full CitComS.py,
e.g.,
\family typewriter
-test-case.cap0.10
+test-case.cap00.10
\family default
.
The first line of the cap file is a comment describing the node geometry
@@ -11452,6 +10753,10 @@
\end_layout
\begin_layout Subsection*
+\begin_inset LatexCommand \label{sub:Velocity-and-Temperature}
+
+\end_inset
+
Velocity and Temperature Output (test-case.velo.0.10)
\end_layout
@@ -11484,7 +10789,10 @@
\end_layout
\begin_layout Standard
-Only output at 0th time step.
+In this version of CitComS.py, the implementation of material support is
+ not working.
+ The material output has been disabled and is documented here for completion.
+ Only output at 0th time step.
There is no header.
The meaning of each column is:
\end_layout
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