[cig-commits] [commit] master: update parameters.tex (4f52fdd)

cig_noreply at geodynamics.org cig_noreply at geodynamics.org
Thu Jan 22 08:16:23 PST 2015 

Repository : https://github.com/geodynamics/aspect

On branch  : master
Link       : https://github.com/geodynamics/aspect/compare/2fcde671ad63cce6d01d453c70d572b875893f2b...59e1a2f9609f8666d604a8513b66c1d5f7b326b8

>---------------------------------------------------------------

commit 4f52fdd537c288e40976177c69c125d166fb5383
Author: Timo Heister <timo.heister at gmail.com>
Date:   Thu Jan 22 09:33:32 2015 -0500

    update parameters.tex


>---------------------------------------------------------------

4f52fdd537c288e40976177c69c125d166fb5383
 doc/manual/parameters.tex | 400 ++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 387 insertions(+), 13 deletions(-)

diff --git a/doc/manual/parameters.tex b/doc/manual/parameters.tex
index 2d12b98..30c7b8a 100644
--- a/doc/manual/parameters.tex
+++ b/doc/manual/parameters.tex
@@ -1433,6 +1433,54 @@ In 3d, inner and outer indicators are treated as in 2d. If the opening angle is
 \label{parameters:Geometry_20model/Box}
 
 \begin{itemize}
+\item {\it Parameter name:} {\tt Box origin X coordinate}
+\phantomsection\label{parameters:Geometry model/Box/Box origin X coordinate}
+
+
+\index[prmindex]{Box origin X coordinate}
+\index[prmindexfull]{Geometry model!Box!Box origin X coordinate}
+{\it Value:} 0
+
+
+{\it Default:} 0
+
+
+{\it Description:} X coordinate of box origin. Units: m.
+
+
+{\it Possible values:} [Double -1.79769e+308...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Box origin Y coordinate}
+\phantomsection\label{parameters:Geometry model/Box/Box origin Y coordinate}
+
+
+\index[prmindex]{Box origin Y coordinate}
+\index[prmindexfull]{Geometry model!Box!Box origin Y coordinate}
+{\it Value:} 0
+
+
+{\it Default:} 0
+
+
+{\it Description:} Y coordinate of box origin. Units: m.
+
+
+{\it Possible values:} [Double -1.79769e+308...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Box origin Z coordinate}
+\phantomsection\label{parameters:Geometry model/Box/Box origin Z coordinate}
+
+
+\index[prmindex]{Box origin Z coordinate}
+\index[prmindexfull]{Geometry model!Box!Box origin Z coordinate}
+{\it Value:} 0
+
+
+{\it Default:} 0
+
+
+{\it Description:} Z coordinate of box origin. This value is ignored if the simulation is in 2d. Units: m.
+
+
+{\it Possible values:} [Double -1.79769e+308...1.79769e+308 (inclusive)]
 \item {\it Parameter name:} {\tt X extent}
 \phantomsection\label{parameters:Geometry model/Box/X extent}
 
@@ -1541,7 +1589,7 @@ In 3d, inner and outer indicators are treated as in 2d. If the opening angle is
 {\it Default:} 1
 
 
-{\it Description:} Extent of the box in z-direction. This value is ignored if the simulation is in 2d Units: m.
+{\it Description:} Extent of the box in z-direction. This value is ignored if the simulation is in 2d. Units: m.
 
 
 {\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
@@ -2996,6 +3044,16 @@ In order to facilitate placing input files in locations relative to the ASPECT s
 
 Otherwise, this material model has a temperature- and pressure-dependent density and viscosity and the density and thermal expansivity depend on the melt fraction present. It is possible to extent this model to include a melt fraction dependence of all the material parameters by calling the function melt\_fraction in the calculation of the respective parameter. However, melt and solid move with the same velocity and melt extraction is not taken into account (batch melting). 
 
+`morency doin': An implementation of the visco-plastic rheology described by (Morency and Doin, 2004). Compositional fields can each be assigned individual activation energies, reference densities, thermal expansivities, and stress exponents. The effective viscosity is defined as
+
+ \[v_{eff} = \left(\frac{1}{v_{eff}^v}+\frac{1}{v_{eff}^p}\right)^{-1}\] where \[v_{eff}^v = B \left(\frac{\dot{\varepsilon}}{\dot{\varepsilon}_{ref}}\right)^{-1+1/n_v} exp\left(\frac{E_a +V_a \rho_m g z}{n_v R T}\right) \] \[v_{eff}^p = (\tau_0 + \gamma \rho_m g z) \left( \frac{\dot{\varepsilon}^{-1+1/n_p}} {\dot{\varepsilon}_{ref}^{1/n_p}} \right) \]
+
+ Where $B$ is a scaling constant, $\dot{\varepsilon}$ is related to the second invariant of the strain rate tensor, $\dot{\varepsilon}_{ref}$ is a reference strain rate, $n_v$ and $n_p$ are stress exponents, $E_a$ is the activation energy, $V_a$ is the activation volume, $\rho_m$ is the mantle density, $R$ is the gas constant, $T$ is temperature, $\tau_0$ is the cohestive strength of rocks at the surface, $\gamma$ is a coefficient of yield stress increase with depth, and $z$ is depth. 
+
+ Morency, C., and M‐P. Doin. "Numerical simulations of the mantle lithosphere delamination." Journal of Geophysical Research: Solid Earth (1978–2012) 109.B3 (2004).
+
+ The value for the components of this formula and additional parameters are read from the parameter file in subsection 'Material model/Morency'.
+
 `multicomponent': This model is for use with an arbitrary number of compositional fields, where each field represents a rock type which can have completely different properties from the others. However, each rock type itself has constant material properties.  The value of the  compositional field is interpreed as a volume fraction. If the sum of the fields is greater than one, they are renormalized.  If it is less than one, material properties  for ``background mantle'' make up the rest. When more than one field is present, the material properties are averaged arithmetically.  An exception is the viscosity, where the averaging should make more of a difference.  For this, the user selects between arithmetic, harmonic, geometric, or maximum composition averaging.
 
 `simple': A material model that has constant values for all coefficients but the density and viscosity. The defaults for all coefficients are chosen to be similar to what is believed to be correct for Earth's mantle. All of the values that define this model are read from a section ``Material model/Simple model'' in the input file, see Section~\ref{parameters:Material_20model/Simple_20model}.
@@ -3023,7 +3081,7 @@ This model uses the following equations for the density: \begin{align}  \rho(p,T
 `table': A material model that reads tables of pressure and temperature dependent material coefficients from files. The default values for this model's runtime parameters use a material description taken from the paper \textit{Complex phase distribution and seismic velocity structure of the transition zone: Convection model predictions for a magnesium-endmember olivine-pyroxene mantle} by Michael H.G. Jacobs and Arie P. van den Berg, Physics of the Earth and Planetary Interiors, Volume 186, Issues 1-2, May 2011, Pages 36--48. See \url{http://www.sciencedirect.com/science/article/pii/S0031920111000422}.
 
 
-{\it Possible values:} [Selection Steinberger|composition reaction|latent heat|latent heat melt|multicomponent|simple|simple compressible|simpler|table ]
+{\it Possible values:} [Selection Steinberger|composition reaction|latent heat|latent heat melt|morency doin|multicomponent|simple|simple compressible|simpler|table ]
 \end{itemize}
 
 
@@ -3722,13 +3780,13 @@ This model uses the following equations for the density: \begin{align}  \rho(p,T
 
 \index[prmindex]{D2}
 \index[prmindexfull]{Material model!Latent heat melt!D2}
-{\it Value:} 1.23e-7
+{\it Value:} 1.329e-7
 
 
-{\it Default:} 1.23e-7
+{\it Default:} 1.329e-7
 
 
-{\it Description:} Prefactor of the linear pressure term in the quadratic function that approximates the solidus of pyroxenite. Units: $°C/Pa$.
+{\it Description:} Prefactor of the linear pressure term in the quadratic function that approximates the solidus of pyroxenite. Note that this factor is different from the value given in Sobolev, 2011, because they use the potential temperature whereas we use the absolute temperature. Units: $°C/Pa$.
 
 
 {\it Possible values:} [Double -1.79769e+308...1.79769e+308 (inclusive)]
@@ -4054,6 +4112,300 @@ This model uses the following equations for the density: \begin{align}  \rho(p,T
 {\it Possible values:} [Double -1.79769e+308...1.79769e+308 (inclusive)]
 \end{itemize}
 
+\subsection{Parameters in section \tt Material model/Morency}
+\label{parameters:Material_20model/Morency}
+
+\begin{itemize}
+\item {\it Parameter name:} {\tt Activation energies}
+\phantomsection\label{parameters:Material model/Morency/Activation energies}
+
+
+\index[prmindex]{Activation energies}
+\index[prmindexfull]{Material model!Morency!Activation energies}
+{\it Value:} 500
+
+
+{\it Default:} 500
+
+
+{\it Description:} List of activation energies, $E_a$, for background mantle and compositional fields,for a total of N+1 values, where N is the number of compositional fields.If only one values is given, then all use the same value.  Units: $kJ / mol$
+
+
+{\it Possible values:} [List list of [Double 0...1.79769e+308 (inclusive)] of length 0...4294967295 (inclusive)]
+\item {\it Parameter name:} {\tt Activation volume}
+\phantomsection\label{parameters:Material model/Morency/Activation volume}
+
+
+\index[prmindex]{Activation volume}
+\index[prmindexfull]{Material model!Morency!Activation volume}
+{\it Value:} 6.4e-6
+
+
+{\it Default:} 6.4e-6
+
+
+{\it Description:} ($V_a$). Units: $m^3 / mol$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Coefficient of yield stress increase with depth}
+\phantomsection\label{parameters:Material model/Morency/Coefficient of yield stress increase with depth}
+
+
+\index[prmindex]{Coefficient of yield stress increase with depth}
+\index[prmindexfull]{Material model!Morency!Coefficient of yield stress increase with depth}
+{\it Value:} 0.25
+
+
+{\it Default:} 0.25
+
+
+{\it Description:} ($\gamma$). Units: None
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Cohesive strength of rocks at the surface}
+\phantomsection\label{parameters:Material model/Morency/Cohesive strength of rocks at the surface}
+
+
+\index[prmindex]{Cohesive strength of rocks at the surface}
+\index[prmindexfull]{Material model!Morency!Cohesive strength of rocks at the surface}
+{\it Value:} 117
+
+
+{\it Default:} 117
+
+
+{\it Description:} ($\tau_0$). Units: $Pa$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Densities}
+\phantomsection\label{parameters:Material model/Morency/Densities}
+
+
+\index[prmindex]{Densities}
+\index[prmindexfull]{Material model!Morency!Densities}
+{\it Value:} 3300.
+
+
+{\it Default:} 3300.
+
+
+{\it Description:} List of densities, $\rho$, for background mantle and compositional fields,for a total of N+1 values, where N is the number of compositional fields.If only one values is given, then all use the same value.  Units: $kg / m^3$
+
+
+{\it Possible values:} [List list of [Double 0...1.79769e+308 (inclusive)] of length 0...4294967295 (inclusive)]
+\item {\it Parameter name:} {\tt Effective viscosity coefficient}
+\phantomsection\label{parameters:Material model/Morency/Effective viscosity coefficient}
+
+
+\index[prmindex]{Effective viscosity coefficient}
+\index[prmindexfull]{Material model!Morency!Effective viscosity coefficient}
+{\it Value:} 1.0
+
+
+{\it Default:} 1.0
+
+
+{\it Description:} Scaling coefficient for effective viscosity.
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Heat capacity}
+\phantomsection\label{parameters:Material model/Morency/Heat capacity}
+
+
+\index[prmindex]{Heat capacity}
+\index[prmindexfull]{Material model!Morency!Heat capacity}
+{\it Value:} 1.25e3
+
+
+{\it Default:} 1.25e3
+
+
+{\it Description:} Units: $J / (K * kg)$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Maximum viscosity}
+\phantomsection\label{parameters:Material model/Morency/Maximum viscosity}
+
+
+\index[prmindex]{Maximum viscosity}
+\index[prmindexfull]{Material model!Morency!Maximum viscosity}
+{\it Value:} 1e28
+
+
+{\it Default:} 1e28
+
+
+{\it Description:} Upper cutoff for effective viscosity. Units: $Pa s$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Minimum strain rate}
+\phantomsection\label{parameters:Material model/Morency/Minimum strain rate}
+
+
+\index[prmindex]{Minimum strain rate}
+\index[prmindexfull]{Material model!Morency!Minimum strain rate}
+{\it Value:} 1.4e-20
+
+
+{\it Default:} 1.4e-20
+
+
+{\it Description:} Stabilizes strain dependent viscosity. Units: $1 / s$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Minimum viscosity}
+\phantomsection\label{parameters:Material model/Morency/Minimum viscosity}
+
+
+\index[prmindex]{Minimum viscosity}
+\index[prmindexfull]{Material model!Morency!Minimum viscosity}
+{\it Value:} 1e17
+
+
+{\it Default:} 1e17
+
+
+{\it Description:} Lower cutoff for effective viscosity. Units: $Pa s$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Preexponential constant for viscous rheology law}
+\phantomsection\label{parameters:Material model/Morency/Preexponential constant for viscous rheology law}
+
+
+\index[prmindex]{Preexponential constant for viscous rheology law}
+\index[prmindexfull]{Material model!Morency!Preexponential constant for viscous rheology law}
+{\it Value:} 1.24e14
+
+
+{\it Default:} 1.24e14
+
+
+{\it Description:} ($B$). Units: None
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Reference strain rate}
+\phantomsection\label{parameters:Material model/Morency/Reference strain rate}
+
+
+\index[prmindex]{Reference strain rate}
+\index[prmindexfull]{Material model!Morency!Reference strain rate}
+{\it Value:} 6.4e-16
+
+
+{\it Default:} 6.4e-16
+
+
+{\it Description:} ($\dot{\varepsilon}_{ref}$). Units: $1 / s$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Reference temperature}
+\phantomsection\label{parameters:Material model/Morency/Reference temperature}
+
+
+\index[prmindex]{Reference temperature}
+\index[prmindexfull]{Material model!Morency!Reference temperature}
+{\it Value:} 293
+
+
+{\it Default:} 293
+
+
+{\it Description:} For calculating density by thermal expansivity. Units: $K$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Reference viscosity}
+\phantomsection\label{parameters:Material model/Morency/Reference viscosity}
+
+
+\index[prmindex]{Reference viscosity}
+\index[prmindexfull]{Material model!Morency!Reference viscosity}
+{\it Value:} 1e22
+
+
+{\it Default:} 1e22
+
+
+{\it Description:} Reference viscosity for nondimensionalization.
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Stress exponents for plastic rheology}
+\phantomsection\label{parameters:Material model/Morency/Stress exponents for plastic rheology}
+
+
+\index[prmindex]{Stress exponents for plastic rheology}
+\index[prmindexfull]{Material model!Morency!Stress exponents for plastic rheology}
+{\it Value:} 30
+
+
+{\it Default:} 30
+
+
+{\it Description:} List of stress exponents, $n_p$, for background mantle and compositional fields,for a total of N+1 values, where N is the number of compositional fields.If only one values is given, then all use the same value.  Units: None
+
+
+{\it Possible values:} [List list of [Double 0...1.79769e+308 (inclusive)] of length 0...4294967295 (inclusive)]
+\item {\it Parameter name:} {\tt Stress exponents for viscous rheology}
+\phantomsection\label{parameters:Material model/Morency/Stress exponents for viscous rheology}
+
+
+\index[prmindex]{Stress exponents for viscous rheology}
+\index[prmindexfull]{Material model!Morency!Stress exponents for viscous rheology}
+{\it Value:} 3
+
+
+{\it Default:} 3
+
+
+{\it Description:} List of stress exponents, $n_v$, for background mantle and compositional fields,for a total of N+1 values, where N is the number of compositional fields.If only one values is given, then all use the same value.  Units: None
+
+
+{\it Possible values:} [List list of [Double 0...1.79769e+308 (inclusive)] of length 0...4294967295 (inclusive)]
+\item {\it Parameter name:} {\tt Thermal diffusivity}
+\phantomsection\label{parameters:Material model/Morency/Thermal diffusivity}
+
+
+\index[prmindex]{Thermal diffusivity}
+\index[prmindexfull]{Material model!Morency!Thermal diffusivity}
+{\it Value:} 0.8e-6
+
+
+{\it Default:} 0.8e-6
+
+
+{\it Description:} Units: $m^2/s$
+
+
+{\it Possible values:} [Double 0...1.79769e+308 (inclusive)]
+\item {\it Parameter name:} {\tt Thermal expansivities}
+\phantomsection\label{parameters:Material model/Morency/Thermal expansivities}
+
+
+\index[prmindex]{Thermal expansivities}
+\index[prmindexfull]{Material model!Morency!Thermal expansivities}
+{\it Value:} 3.5e-5
+
+
+{\it Default:} 3.5e-5
+
+
+{\it Description:} List of thermal expansivities for background mantle and compositional fields,for a total of N+1 values, where N is the number of compositional fields.If only one values is given, then all use the same value.  Units: $1 / K$
+
+
+{\it Possible values:} [List list of [Double 0...1.79769e+308 (inclusive)] of length 0...4294967295 (inclusive)]
+\end{itemize}
+
 \subsection{Parameters in section \tt Material model/Multicomponent}
 \label{parameters:Material_20model/Multicomponent}
 
@@ -5900,13 +6252,13 @@ As stated, this postprocessor computes the \textit{outbound} heat flux. If you a
 
 \index[prmindex]{Number of zones}
 \index[prmindexfull]{Postprocess!Depth average!Number of zones}
-{\it Value:} 100
+{\it Value:} 10
 
 
-{\it Default:} 100
+{\it Default:} 10
 
 
-{\it Description:} The number of zones in depth direction within which we are to compute averages. By default, we subdivide the entire domain into 100 depth zones and compute temperature and other averages within each of these zones. However, if you have a very coarse mesh, it may not make much sense to subdivide the domain into so many zones and you may wish to choose less than this default. It may also make computations slightly faster. On the other hand, if you have an extremely highly resolved mesh, choosing more zones might also make sense.
+{\it Description:} The number of zones in depth direction within which we are to compute averages. By default, we subdivide the entire domain into 10 depth zones and compute temperature and other averages within each of these zones. However, if you have a very coarse mesh, it may not make much sense to subdivide the domain into so many zones and you may wish to choose less than this default. It may also make computations slightly faster. On the other hand, if you have an extremely highly resolved mesh, choosing more zones might also make sense.
 
 
 {\it Possible values:} [Integer range 1...2147483647 (inclusive)]
@@ -5976,10 +6328,10 @@ As stated, this postprocessor computes the \textit{outbound} heat flux. If you a
 
 \index[prmindex]{Data output format}
 \index[prmindexfull]{Postprocess!Tracers!Data output format}
-{\it Value:} none
+{\it Value:} vtu
 
 
-{\it Default:} none
+{\it Default:} vtu
 
 
 {\it Description:} File format to output raw particle data in.
@@ -6042,6 +6394,28 @@ Units: years if the 'Use years in output instead of seconds' parameter is set; s
 \label{parameters:Postprocess/Visualization}
 
 \begin{itemize}
+\item {\it Parameter name:} {\tt Interpolate output}
+\phantomsection\label{parameters:Postprocess/Visualization/Interpolate output}
+
+
+\index[prmindex]{Interpolate output}
+\index[prmindexfull]{Postprocess!Visualization!Interpolate output}
+{\it Value:} false
+
+
+{\it Default:} false
+
+
+{\it Description:} deal.II offers the possibility to linearly interpolate output fields of higher order elements to a finer resolution. This somewhat compensates the fact that most visualization software only offers linear interpolation between grid points and therefore the output file is a very coarse representation of the actual solution field. Activating this option increases the spatial resolution in each dimension by a factor equal to the polynomial degree used for the velocity finite element (usually 2). In other words, instead of showing one quadrilateral or hexahedron in the visualization per cell on which \aspect{} computes, it shows multiple (for quadratic elements, it will describe each cell of the mesh on which we compute as $2\times 2$ or $2\times 2\times 2$ cells in 2d and 3d, respectively; correspondingly more subdivisions are used if you use cubic, quartic, or even higher order elements for the velocity).
+
+The effect of using this option can be seen in the following picture showing a variation of the output produced with the input files from Section~\ref{sec:shell-simple-2d}:
+
+\begin{center}  \includegraphics[width=0.5\textwidth]{viz/parameters/build-patches}\end{center}Here, the left picture shows one visualization cell per computational cell (i.e., the option is switch off, as is the default), and the right picture shows the same simulation with the option switched on. The images show the same data, demonstrating that interpolating the solution onto bilinear shape functions as is commonly done in visualizing data loses information.
+
+Of course, activating this option also greatly increases the amount of data \aspect{} will write to disk: approximately by a factor of 4 in 2d, and a factor of 8 in 3d, when using quadratic elements for the velocity, and correspondingly more for even higher order elements.
+
+
+{\it Possible values:} [Bool]
 \item {\it Parameter name:} {\tt List of output variables}
 \phantomsection\label{parameters:Postprocess/Visualization/List of output variables}
 
@@ -6374,13 +6748,13 @@ viscosity|density|thermal expansivity|specific heat|thermal conductivity|compres
 
 \index[prmindex]{D2}
 \index[prmindexfull]{Postprocess!Visualization!Melt fraction!D2}
-{\it Value:} 1.23e-7
+{\it Value:} 1.329e-7
 
 
-{\it Default:} 1.23e-7
+{\it Default:} 1.329e-7
 
 
-{\it Description:} Prefactor of the linear pressure term in the quadratic function that approximates the solidus of pyroxenite. Units: $°C/Pa$.
+{\it Description:} Prefactor of the linear pressure term in the quadratic function that approximates the solidus of pyroxenite. Note that this factor is different from the value given in Sobolev, 2011, because they use the potential temperature whereas we use the absolute temperature. Units: $°C/Pa$.
 
 
 {\it Possible values:} [Double -1.79769e+308...1.79769e+308 (inclusive)]

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