[cig-commits] r14689 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Mon Apr 13 17:34:17 PDT 2009
Author: tan2
Date: 2009-04-13 17:34:17 -0700 (Mon, 13 Apr 2009)
New Revision: 14689
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Editing Cookbook 2-4 and some appendix.
* Explained how to define domain size in Cookbook 2.
* Explained the viscosity law in Cookbook 3.
* Removed domain size definition in Cookbook 4, since the size is defined by coor_file actually.
* Documented all "tic_method" and "rheol" options.
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2009-04-14 00:28:38 UTC (rev 14688)
+++ doc/CitcomS/manual/citcoms.lyx 2009-04-14 00:34:17 UTC (rev 14689)
@@ -7943,8 +7943,8 @@
\begin_layout Standard
Cookbooks 1 to 4 introduce the basic parameters and are suitable for all
users.
- Cookbook 5 introduces time-dependent velocity boundary conditions and tuning
- of the advection solver.
+ Cookbook 5 introduces time-dependent velocity boundary conditions, reading
+ in initial temperature field from files and tuning of the advection solver.
Cookbook 6 introduces the pseudo-free-surface formulation for studying
short wavelength dynamics topography.
Cookbook 7 introduces thermo-chemical convection problem and tuning of
@@ -8218,15 +8218,11 @@
\begin_layout Standard
This is not particularly efficient, but it does illustrate the flexibility
- of both
-\family typewriter
-mpi
-\family default
- and Pyre.
+ of both MPI and Pyre.
\end_layout
\begin_layout Section
-Cookbook 2: Velocity Boundary Conditions
+Cookbook 2: Domain Size and Velocity Boundary Conditions
\end_layout
\begin_layout Subsection
@@ -8276,7 +8272,53 @@
Continue to use the default values for the physical portion of the domain
in which you are interested.
However, try modifying the layout of the mesh as shown.
-
+ The parameters specify two processors per cap in the
+\begin_inset Formula $x$
+\end_inset
+
+- and
+\begin_inset Formula $y$
+\end_inset
+
+-direction, one processor per cap in the
+\begin_inset Formula $z$
+\end_inset
+
+-direction (by default), 17 nodes per cap in the
+\begin_inset Formula $x$
+\end_inset
+
+- and
+\begin_inset Formula $y$
+\end_inset
+
+-direction, 9 nodes in the
+\begin_inset Formula $z$
+\end_inset
+
+-direction, and the minimum/maximum extents in the colatitudal, longitudal,
+ and radial (
+\family typewriter
+theta
+\family default
+,
+\family typewriter
+fi
+\family default
+,
+\family typewriter
+radius
+\family default
+) directions.
+ The unit for
+\family typewriter
+theta
+\family default
+ and
+\family typewriter
+fi
+\family default
+ is radian.
\end_layout
\begin_layout LyX-Code
@@ -8289,6 +8331,21 @@
nodey = 17
\newline
nodez = 9
+\newline
+
+\newline
+theta_min = 0.7854
+\newline
+theta_ma
+x = 1.5708
+\newline
+fi_min = 0.0
+\newline
+fi_max = 0.7854
+\newline
+radius_inner = 0.55
+\newline
+radius_outer = 1.0
\end_layout
\begin_layout Standard
@@ -8305,7 +8362,6 @@
\end_inset
for how to dimensionalize it).
-
\end_layout
\begin_layout LyX-Code
@@ -8378,12 +8434,27 @@
\newline
\newline
+theta_min = 0.7854
+\newline
+theta_max = 1.5708
+\newline
+fi_min = 0.0
+\newline
+fi_max = 0.7854
+\newline
+radius_inner
+ = 0.55
+\newline
+radius_outer = 1.0
+\newline
+
+\newline
# Impose a uniform velocity across the top surface.
\newline
-[CitcomS.solver.bc]
+[Citcom
+S.solver.bc]
\newline
-topvbc
- = 1
+topvbc = 1
\newline
topvbxval = 100
\newline
@@ -8391,15 +8462,15 @@
\newline
\newline
-# In addition, set the initial temperatur
-e perturbation to zero.
+# In addition, set
+ the initial temperature perturbation to zero.
\newline
[CitcomS.solver.ic]
\newline
-num_perturbations = 1
+num_perturbations
+ = 1
\newline
-perturbmag
- = 0.0
+perturbmag = 0.0
\end_layout
\begin_layout Subsection
@@ -8527,8 +8598,9 @@
\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 (
+), the type of viscosity law to use (4), the activation energy of each layer
+ (0.2,0.2,0.2,0.2), the temperature offset of each layer (0,0,0,0), the activation
+ volume of each layer (0,0,0,0), whether to apply the minimum cutoff (
\family typewriter
on
\family default
@@ -8550,18 +8622,23 @@
\newline
TDEPV = on
\newline
+rheol = 4
+\newline
viscE = 0.2,0.2,0.2,0.2
\newline
-viscT
- = 0,0,0,0
+
+viscT = 0,0,0,0
\newline
+viscZ = 0,0,0,0
+\newline
VMIN = on
\newline
visc_min = 1.0
\newline
VMAX = on
\newline
-visc_max = 100.0
+visc_max =
+ 100.0
\end_layout
\begin_layout Standard
@@ -8582,17 +8659,107 @@
\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
+ These depth parameters also control the depth of various phase transitions.
+\end_layout
+
+\begin_layout Standard
+There are several viscosity laws coded in the program, which can be selected
+ by the
+\family typewriter
+rheol
+\family default
+ parameter.
+ All available viscosity laws can be found in Appendix
+\begin_inset LatexCommand ref
+reference "sub:Viscosity-input"
+
+\end_inset
+
+.
+ For
+\family typewriter
+rheol=4
+\family default
+, the temperature dependence of the viscosity of each layer is determined
by:
\end_layout
\begin_layout Standard
\begin_inset Formula \begin{equation}
-visc=visc0\times exp\left(\frac{viscE}{T+viscT}-\frac{viscE}{1+viscT}\right)\label{eq:22}\end{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
+This equation is non-dimensionalized.
+ The last term on the right-hand-side is to normalize the viscosity so that
+
+\begin_inset Formula $visc=visc0$
+\end_inset
+ when
+\begin_inset Formula $T=1$
+\end_inset
+
+ and
+\begin_inset Formula $r=r_{inner}$
+\end_inset
+
+.
+ Comparing Equation
+\begin_inset LatexCommand ref
+reference "eq:non-dim visc law"
+
+\end_inset
+
+ with the dimensional Arrhenius activation equation:
+\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}
+
+\end_inset
+
+where
+\begin_inset Formula $E_{a}$
+\end_inset
+
+ and
+\begin_inset Formula $V_{a}$
+\end_inset
+
+ are the activation energy and activation volume,
+\begin_inset Formula $P$
+\end_inset
+
+ is the hydrostatic pressure,
+\begin_inset Formula $R$
+\end_inset
+
+ is the universal gas constant, and other symbols are as defined in Section
+
+\begin_inset LatexCommand ref
+reference "sec:Governing-Equations"
+
+\end_inset
+
+, it is clear that
+\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}
+
+\end_inset
+
+
+\begin_inset Formula \begin{equation}
+viscT=T_{0}\label{eq:viscT}\end{equation}
+
+\end_inset
+
+
\end_layout
\begin_layout Subsubsection
@@ -8655,16 +8822,21 @@
\newline
TDEPV = on
\newline
-viscE =
- 0.2,0.2,0.2,0.2
+rheol =
+ 4
\newline
+viscE = 0.2,0.2,0.2,0.2
+\newline
viscT = 0,0,0,0
\newline
+viscZ = 0,0,0,0
+\newline
VMIN = on
\newline
visc_min = 1.0
\newline
-VMAX = on
+VMAX
+ = on
\newline
visc_max = 100.0
\end_layout
@@ -8766,24 +8938,14 @@
\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.
+ in latitude between radian 0 and 1, and in radius between 0.55 and 1, as
+ determined by the content of
+\family typewriter
+coor_file
+\family default
+.
\end_layout
-\begin_layout LyX-Code
-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 Subsubsection
Example: Regionally Refined Meshes,
\family typewriter
@@ -8860,19 +9022,6 @@
\newline
nodez = 17
\newline
-theta_min = 1
-\newline
-theta_max = 2
-\newline
-fi_min
- = 0
-\newline
-fi_max = 1
-\newline
-radius_inner = 0.55
-\newline
-radius_outer = 1
-\newline
\newline
[CitcomS.solver.visc]
@@ -8886,13 +9035,17 @@
\newline
TDEPV = on
\newline
+rheol = 4
+\newline
viscE = 0.2,0.2,0.2,0.2
\newline
-viscT = 0,0,0,0
+viscT
+ = 0,0,0,0
\newline
-VMIN
- = on
+viscZ = 0,0,0,0
\newline
+VMIN = on
+\newline
visc_min = 1.0
\newline
VMAX = on
@@ -12906,7 +13059,7 @@
\begin_layout Standard
\align left
\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="2">
+<lyxtabular version="3" rows="3" columns="2">
<features>
<column alignment="left" valignment="top" leftline="true" width="1.85in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="4.25in">
@@ -12952,7 +13105,7 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
@@ -13095,11 +13248,26 @@
perturbm=1
\newline
perturblayer=5
+\newline
+
+\newline
+half_space_ag
+e=40
+\newline
+mantle_temp=1.0
+\newline
+
+\newline
+blob_center=[-999,-999,-999]
+\newline
+blob_radius=0.063
+\newline
+blob_dT=0.18
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
@@ -13111,49 +13279,98 @@
\family default
\size default
.
- The initial temperature is a linear temperature gradient with some perturbation
-s, and
+ The initial temperature is a linear temperature gradient with perturbations
+ at specific layers, where
\family typewriter
num_perturbations
\family default
- specifies the number of perturbations.
- The amplitude of the perturbations is specified in the list of real numbers
- by
+ specifies the number of perturbations, and
\family typewriter
-perturbmag
+perturblayer
\family default
-.
- In a full spherical model,
+ specifies the layers to be perturbed, representing the number of the mesh
+ node in radial direction.
+ There must be as many entries as
\family typewriter
-perturbl
+num_perturbations
\family default
- and
+ in a comma-separated list.
+ The perturbation added to each layer is given by:
+\begin_inset Formula \[
+mag\times\cos(m\phi)\times P_{lm}(\cos\theta)\]
+
+\end_inset
+
+for the full sphere, and by:
+\begin_inset Formula \[
+mag\times\cos(\frac{\left(\theta-\theta_{min}\right)l\pi}{\theta_{max}-\theta_{min}})\times\cos(\frac{\left(\phi-\phi_{min}\right)m\pi}{\phi_{max}-\phi_{min}})\]
+
+\end_inset
+
+for the regional sphere.
+\newline
+If
\family typewriter
-perturbm
+tic_method
+\size small
+=
\family default
- specify the shape of the perturbations in spherical harmonic degree and
- order.
- In a regional model,
+\size default
+1, T is
\family typewriter
-perturbl
+1
\family default
- and
+ everywhere, except a cold thermal boundary layer at the top, whose temperature
+ is determined by the half-space cooling model and
\family typewriter
-preturbm
+\size small
+half_space_age
\family default
- specify the number of nodal lines in longitudinal and latitudinal directions.
+\size default
+ (in million of years, Myrs).
+\newline
+If
\family typewriter
-perturblayer
+tic_method
+\size small
+=2,
\family default
- specifies the layers to be perturbed, representing the number of the mesh
- node in radial direction.
- There must be as many entries as
+\size default
+ T is
\family typewriter
-num_perturbations
+\size small
+mantle_temp
\family default
- in a comma-separated list.
-\newline
+\size default
+ everywhere, except a warm spherical blob and a cold thermal boundary layer
+ at the top, whose temperature is determined by the half-space cooling model
+ and
+\family typewriter
+\size small
+half_space_age
+\family default
+\size default
+ (in Myrs)
+\family roman
+\series medium
+\shape up
+\size normal
+\emph off
+\bar no
+\noun off
+\color none
+.
+ The location of the blob is default to the center of the computational
+ domain.
+\family default
+\series default
+\shape default
+\size default
+\emph default
+\bar default
+\noun default
+\color inherit
\newline
If
@@ -13163,74 +13380,108 @@
=
\family default
\size default
-3.
- The initial temperature is a conductive profile with some perturbations.
+3, the initial temperature is a conductive profile with perturbations to
+ all layers.
The perturbation is given by:
\begin_inset Formula \[
mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)\]
\end_inset
+for the full sphere, and by:
+\begin_inset Formula \[
+mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\times\cos(\frac{\left(\theta-\theta_{min}\right)l\pi}{\theta_{max}-\theta_{min}})\times\cos(\frac{\left(\phi-\phi_{min}\right)m\pi}{\phi_{max}-\phi_{min}})\]
-\end_layout
-
\end_inset
-</cell>
-</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-\begin_layout Standard
-
+for the regional sphere.
+\newline
+If
\family typewriter
+tic_method
\size small
-half_space_age=40
+=
+\family default
+\size default
+4, the initial temperature is read fro grd files.
\newline
-mantle_temp=1.0
+If
+\family typewriter
+tic_method
+\size small
+=10,
+\family default
+\size default
+ T is
+\family typewriter
+\size small
+mantle_temp
+\family default
+\size default
+ everywhere, except a cold thermal boundary layer at the top and perturbations
+ at all layers, similar to
+\family typewriter
+tic_method=3
+\family default
+.
\newline
-blob_center=[-999,-999,-999]
+If
+\family typewriter
+tic_method
+\size small
+=11,
+\family default
+\size default
+ T is
+\family typewriter
+\size small
+mantle_temp
+\family default
+\size default
+ everywhere, except a hot thermal boundary layer at the bottom and perturbations
+ at all layers, similar to
+\family typewriter
+tic_method=3
+\family default
+.
\newline
-blob_radius=0.063
-\newline
-blob_
-dT=0.18
+If
+\family typewriter
+tic_method
+\size small
+=12,
+\family default
+\size default
+ T is
+\family typewriter
+\size small
+mantle_temp
+\family default
+\size default
+ everywhere, except a cold thermal boundary layer, a hot thermal boundary
+ layer at the bottom and perturbations at all layers, similar to
+\family typewriter
+tic_method=3
+\family default
+.
\end_layout
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
\begin_layout Standard
-Used only if
+If
\family typewriter
tic_method
\size small
-=2
+=90,
\family default
\size default
- and in the regional model.
- This creates a top thermal boundary with a half-space cooling age specified
- by
+ T is
\family typewriter
-half_space_age
+\size small
+0
\family default
- in millions of years and a warm spherical blob
-\family roman
-\series medium
-\shape up
-\size normal
-\emph off
-\bar no
-\noun off
-\color none
-.
- These parameters specify the temperature of the ambient mantle, the location
- and radius of the blob, and also the amplitude of temperature change in
- the blob relative to the ambient mantle temperautre.
- The location of the blob is default to the center of the computational
- domain.
+\size default
+ everywhere, except a single perturbation at the middel layer.
+ This initial temperature is good for comparison with analytical solutions.
\end_layout
\end_inset
@@ -13699,6 +13950,12 @@
\begin_layout Subsection
Viscosity
+\begin_inset LatexCommand label
+name "sub:Viscosity-input"
+
+\end_inset
+
+
\end_layout
\begin_layout Standard
@@ -13925,7 +14182,7 @@
\family typewriter
\size footnotesize
-\begin_inset Formula $\eta=\eta_{0}\times\exp(\eta_{E}(\eta_{T}-T))$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(E{}_{\eta}(T_{\eta}-T))$
\end_inset
@@ -13941,7 +14198,7 @@
\family typewriter
\size footnotesize
-\begin_inset Formula $\eta=\eta_{0}\times\exp(-\frac{T}{\eta_{T}})$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(-T/T_{\eta})$
\end_inset
@@ -13953,11 +14210,11 @@
\family typewriter
rheol
\family default
-=3 or 5, temperature-dependent viscosity is computed by
+=3, temperature-dependent viscosity is computed by
\family typewriter
\size footnotesize
-\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{\eta_{E}}{T+\eta_{T}}-\frac{\eta_{E}}{1+\eta_{T}})$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{E_{\eta}}{T+T_{\eta}}-\frac{E_{\eta}}{1+T_{\eta}})$
\end_inset
@@ -13973,7 +14230,7 @@
\family typewriter
\size footnotesize
-\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{\eta_{E}+\eta_{Z}(1-r)}{T+\eta_{T}})$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{E_{\eta}+Z_{\eta}(1-r)}{T+T_{\eta}})$
\end_inset
@@ -13985,11 +14242,27 @@
\family typewriter
rheol
\family default
+=5, same as
+\family typewriter
+rheol
+\family default
+=3, except the viscosity cut-off is applied before
+\family typewriter
+mat_control
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+When
+\family typewriter
+rheol
+\family default
=6, temperature-dependent viscosity is computed by
\family typewriter
\size footnotesize
-\begin_inset Formula $\eta=\eta_{0}\times\exp(\eta_{E}(\eta_{T}-T)+(1-r)\eta_{Z})$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(E_{\eta}(T_{\eta}-T)+Z_{\eta}(1-r))$
\end_inset
@@ -14005,7 +14278,7 @@
\family typewriter
\size footnotesize
-\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{\eta_{E}+\eta_{Z}(1-r)}{T+\eta_{T}}-\frac{\eta_{E}+\eta_{Z}(1-r_{inner})}{1+\eta_{T}})$
+\begin_inset Formula $\eta=\eta_{0}\times\exp(\frac{E_{\eta}+Z_{\eta}(1-r)}{T+T_{\eta}}-\frac{E_{\eta}+Z_{\eta}(1-r_{inner})}{1+T_{\eta}})$
\end_inset
@@ -14016,6 +14289,17 @@
\end_inset
is the inner radius of the mesh.
+\newline
+When
+\family typewriter
+rheol
+\family default
+=8, same as
+\family typewriter
+rheol
+\family default
+=3, except viscosity reduction is applied when the temperature exceeds the
+ solidus.
\end_layout
\end_inset
@@ -14043,15 +14327,15 @@
\begin_layout Standard
Parameters defining viscosity law (
-\begin_inset Formula $\eta_{E}$
+\begin_inset Formula $E_{\eta}$
\end_inset
,
-\begin_inset Formula $\eta_{T}$
+\begin_inset Formula $T_{\eta}$
\end_inset
, and
-\begin_inset Formula $\eta_{Z}$
+\begin_inset Formula $Z_{\eta}$
\end_inset
in the equations above, respectively).
More information about the CIG-COMMITS
mailing list