[cig-commits] commit 2306 by bangerth to /var/svn/dealii/aspect
dealii.demon at gmail.com
dealii.demon at gmail.com
Mon Feb 17 11:16:23 PST 2014
Revision 2306
Annotate some parameter files. Add a couple of new ones. Move those that haven't been used in the manual into future/.
U trunk/aspect/cookbooks/composition-active.prm
U trunk/aspect/cookbooks/composition-passive-tracers.prm
U trunk/aspect/cookbooks/composition-passive.prm
U trunk/aspect/cookbooks/convection-box-3d.prm
U trunk/aspect/cookbooks/convection-box.prm
A trunk/aspect/cookbooks/future/inclusion.prm
A trunk/aspect/cookbooks/future/periodic_box.prm
D trunk/aspect/cookbooks/future/simple_2d_shell.prm
A trunk/aspect/cookbooks/future/table_model.prm
D trunk/aspect/cookbooks/inclusion.prm
D trunk/aspect/cookbooks/periodic_box.prm
U trunk/aspect/cookbooks/platelike-boundary.prm
A trunk/aspect/cookbooks/shell_simple_2d.prm
A trunk/aspect/cookbooks/shell_simple_3d.prm
U trunk/aspect/cookbooks/sol_cx.prm
U trunk/aspect/cookbooks/sol_kz.prm
U trunk/aspect/cookbooks/stokes.prm
D trunk/aspect/cookbooks/table_model.prm
http://www.dealii.org/websvn/revision.php?repname=Aspect+Repository&path=%2F&rev=2306&peg=2306
Diff:
Modified: trunk/aspect/cookbooks/composition-active.prm
===================================================================
--- trunk/aspect/cookbooks/composition-active.prm 2014-02-17 18:40:09 UTC (rev 2305)
+++ trunk/aspect/cookbooks/composition-active.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -1,8 +1,11 @@
#########################################################
-# This is a variation of the platelike-boundary.prm file.
-# All settings are exactly the same with the exception
-# of the ones that pertain to compositional fields.
+# This is a variation of the composition-passive.prm file.
+# Here, we choose a higher Rayleigh number and make the
+# density depend on the compositional variable as well.
+#
+# See the manual for more information about this setup.
+
set Dimension = 2
set Start time = 0
set End time = 20
Modified: trunk/aspect/cookbooks/composition-passive-tracers.prm
===================================================================
--- trunk/aspect/cookbooks/composition-passive-tracers.prm 2014-02-17 18:40:09 UTC (rev 2305)
+++ trunk/aspect/cookbooks/composition-passive-tracers.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -4,7 +4,10 @@
# advect along a set of tracers and that we do not longer
# compute temperature statistics and composition statistics
# as part of postprocessing
+#
+# See the manual for more information about this setup.
+
set Dimension = 2
set Start time = 0
set End time = 20
Modified: trunk/aspect/cookbooks/composition-passive.prm
===================================================================
--- trunk/aspect/cookbooks/composition-passive.prm 2014-02-17 18:40:09 UTC (rev 2305)
+++ trunk/aspect/cookbooks/composition-passive.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -2,7 +2,10 @@
# This is a variation of the platelike-boundary.prm file.
# All settings are exactly the same with the exception
# of the ones that pertain to compositional fields.
+#
+# See the manual for more information about this setup.
+
set Dimension = 2
set Start time = 0
set End time = 20
Modified: trunk/aspect/cookbooks/convection-box-3d.prm
===================================================================
--- trunk/aspect/cookbooks/convection-box-3d.prm 2014-02-17 18:40:09 UTC (rev 2305)
+++ trunk/aspect/cookbooks/convection-box-3d.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -1,3 +1,5 @@
+# A description of convection in a 3d box. See the manual for more information.
+
# At the top, we define the number of space dimensions we would like to
# work in:
set Dimension = 3
Modified: trunk/aspect/cookbooks/convection-box.prm
===================================================================
--- trunk/aspect/cookbooks/convection-box.prm 2014-02-17 18:40:09 UTC (rev 2305)
+++ trunk/aspect/cookbooks/convection-box.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -1,3 +1,6 @@
+# A description of convection in a 2d box. See the manual for more information.
+
+
# At the top, we define the number of space dimensions we would like to
# work in:
set Dimension = 2
Copied: trunk/aspect/cookbooks/future/inclusion.prm (from rev 2304, trunk/aspect/cookbooks/inclusion.prm)
===================================================================
--- trunk/aspect/cookbooks/future/inclusion.prm (rev 0)
+++ trunk/aspect/cookbooks/future/inclusion.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -0,0 +1,77 @@
+############### Global parameters
+
+set Dimension = 2
+
+set Start time = 0
+set End time = 0
+
+set Output directory = output
+
+set Pressure normalization = volume
+
+
+############### Parameters describing the model
+
+subsection Geometry model
+ set Model name = box
+
+ subsection Box
+ set X extent = 2
+ set Y extent = 2
+ end
+end
+
+
+subsection Model settings
+ set Prescribed velocity boundary indicators = 0:inclusion, 1:inclusion, 2:inclusion, 3:inclusion
+ set Tangential velocity boundary indicators =
+ set Zero velocity boundary indicators =
+end
+
+
+subsection Material model
+ set Model name = Inclusion
+
+ subsection Inclusion
+ set Viscosity jump = 1e3
+ end
+end
+
+
+subsection Gravity model
+ set Model name = vertical
+end
+
+
+############### Parameters describing the temperature field
+
+subsection Boundary temperature model
+ set Model name = box
+end
+
+
+subsection Initial conditions
+ set Model name = perturbed box
+end
+
+
+
+############### Parameters describing the discretization
+
+subsection Discretization
+ set Stokes velocity polynomial degree = 2
+ set Use locally conservative discretization = false
+end
+
+
+subsection Mesh refinement
+ set Initial adaptive refinement = 0
+ set Initial global refinement = 6
+end
+
+
+############### Parameters describing the what to do with the solution
+
+subsection Postprocess
+ set List of postprocessors = DuretzEtAl error, visualization
+end
Copied: trunk/aspect/cookbooks/future/periodic_box.prm (from rev 2304, trunk/aspect/cookbooks/periodic_box.prm)
===================================================================
--- trunk/aspect/cookbooks/future/periodic_box.prm (rev 0)
+++ trunk/aspect/cookbooks/future/periodic_box.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -0,0 +1,105 @@
+set Dimension = 2
+set CFL number = 1.0
+set End time = 1e9
+set Output directory = output
+set Resume computation = false
+set Start time = 0
+set Adiabatic surface temperature = 0
+set Surface pressure = 0
+set Pressure normalization = no
+set Linear solver tolerance = 1.e-7
+set Use years in output instead of seconds = true
+set Nonlinear solver scheme = IMPES
+
+subsection Boundary temperature model
+ set Model name = box
+ subsection Box
+ set Top temperature = 0.0
+ set Bottom temperature = 1000.0
+ end
+end
+
+
+subsection Discretization
+ set Stokes velocity polynomial degree = 2
+ set Temperature polynomial degree = 2
+ set Use locally conservative discretization = false
+ subsection Stabilization parameters
+ set alpha = 2
+ set beta = 0.078
+ set cR = 0.5 # default: 0.11
+ end
+end
+
+
+subsection Geometry model
+ set Model name = box
+ subsection Box
+ set X periodic = true
+ set X extent = 1.e6
+ set Y extent = 5.e5
+ set Z extent = 5.e5
+ end
+end
+
+
+subsection Gravity model
+ set Model name = vertical
+ subsection Vertical
+ set Magnitude = 10.0
+ end
+end
+
+
+subsection Initial conditions
+ set Model name = function
+ subsection Function
+ set Variable names = x,y
+ set Function expression = if((sqrt((x-1.e5)^2+(y-4.0e5)^2)<5.0e4) | (sqrt((x-3.e5)^2+(y-2.e5)^2)<1.0e5) , 800.0, 0)
+ end
+end
+
+
+subsection Material model
+ set Model name = simple
+ subsection Simple model
+ set Reference density = 3300
+ set Reference specific heat = 1250
+ set Reference temperature = 0.0
+ set Thermal conductivity = 4.7
+ set Thermal expansion coefficient = 4e-5
+ set Viscosity = 1.e20
+ end
+end
+
+
+subsection Mesh refinement
+ set Additional refinement times =
+ set Initial adaptive refinement = 2 # default: 2
+ set Initial global refinement = 6 # default: 2
+ set Refinement fraction = 0.3
+ set Coarsening fraction = 0.03
+ set Strategy = thermal energy density
+ set Time steps between mesh refinement = 10 # default: 10
+end
+
+
+subsection Model settings
+ set Include adiabatic heating = false
+ set Include shear heating = false
+ set Radiogenic heating rate = 0
+ set Fixed temperature boundary indicators = 2,3
+ set Prescribed velocity boundary indicators =
+ set Tangential velocity boundary indicators =
+ set Zero velocity boundary indicators = 2,3
+end
+
+subsection Postprocess
+ set List of postprocessors = visualization
+ subsection Visualization
+ set List of output variables =
+ set Number of grouped files = 1
+ set Output format = vtu
+ set Time between graphical output = 1.e5
+ end
+end
Copied: trunk/aspect/cookbooks/future/table_model.prm (from rev 2304, trunk/aspect/cookbooks/table_model.prm)
===================================================================
--- trunk/aspect/cookbooks/future/table_model.prm (rev 0)
+++ trunk/aspect/cookbooks/future/table_model.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -0,0 +1,139 @@
+set Adiabatic surface temperature = 0
+set CFL number = 1.0
+set Dimension = 2
+set End time = 1e12 # default: 1e8
+set Linear solver tolerance = 1e-7
+set Nonlinear solver scheme = IMPES
+set Output directory = output
+set Pressure normalization = surface
+set Resume computation = false
+set Start time = 0
+set Surface pressure = 0
+set Temperature solver tolerance = 1e-12
+set Timing output frequency = 100
+set Use years in output instead of seconds = true
+
+subsection Boundary temperature model
+ set Model name = spherical constant # default:
+ subsection Spherical constant
+ set Inner temperature = 4273 # default: 6000
+ set Outer temperature = 973 # default: 0
+ end
+end
+
+subsection Checkpointing
+ set Steps between checkpoint = 0
+ set Time between checkpoint = 0
+end
+
+subsection Discretization
+ set Stokes velocity polynomial degree = 2
+ set Temperature polynomial degree = 2
+ set Use locally conservative discretization = false
+ subsection Stabilization parameters
+ set alpha = 2
+ set beta = 0.078
+ set cR = 0.11
+ end
+end
+
+subsection Geometry model
+ set Model name = spherical shell # default:
+ subsection Spherical shell
+ set Inner radius = 3481000
+ set Opening angle = 90 # default: 360
+ set Outer radius = 6336000
+ end
+end
+
+subsection Gravity model
+ set Model name = radial earth-like # default:
+end
+
+subsection Initial conditions
+ set Model name = spherical hexagonal perturbation # default:
+end
+
+subsection Material model
+ set Model name = table # default:
+ subsection Table model
+ set Composition = standard
+ set Compressible = true
+ set ComputePhases = false
+ set Gravity = 30
+ set Path to model data = data/material-model/table/
+ set Reference density = 3300
+ set Reference specific heat = 1250
+ set Reference temperature = 293
+ set Thermal conductivity = 4.7
+ set Thermal expansion coefficient = 2e-5
+ subsection Viscosity
+ set Reference Viscosity = 5e24
+ set Viscosity increase lower mantle = 1e0
+ set Viscosity Model = Exponential
+ subsection Composite
+ set Activation energy diffusion = 335e3
+ set Activation energy dislocation = 540e3
+ set Activation volume diffusion = 4.0e-6
+ set Activation volume dislocation = 14.0e-6
+ set Prefactor diffusion = 1.92e-11
+ set Prefactor dislocation = 2.42e-10
+ set Stress exponent = 3.5
+ end
+ subsection Diffusion
+ set Activation energy diffusion = 335e3
+ set Activation volume diffusion = 4.0e-6
+ set Prefactor diffusion = 1.92e-11
+ end
+ subsection Dislocation
+ set Activation energy dislocation = 335e3
+ set Activation volume dislocation = 4.0e-6
+ set Prefactor dislocation = 1.92e-11
+ set Stress exponent = 3.5
+ end
+ subsection Exponential
+ set Exponential P = 1
+ set Exponential T = 1
+ end
+ end
+ end
+end
+
+subsection Mesh refinement
+ set Additional refinement times =
+ set Coarsening fraction = 0.05
+ set Initial adaptive refinement = 3 # default: 2
+ set Initial global refinement = 4 # default: 2
+ set Refinement fraction = 0.3
+ set Run postprocessors on initial refinement = false
+ set Strategy = temperature # default: Density c_p temperature
+ set Time steps between mesh refinement = 5 # default: 10
+end
+
+subsection Model settings
+ set Fixed temperature boundary indicators = 0,1 # default:
+ set Include adiabatic heating = false
+ set Include shear heating = true
+ set Prescribed velocity boundary indicators =
+ set Radiogenic heating rate = 0e0
+ set Tangential velocity boundary indicators = 1,2,3 # default:
+ set Zero velocity boundary indicators = 0 # default:
+end
+
+subsection Postprocess
+ set List of postprocessors = visualization,velocity statistics,temperature statistics,heat flux statistics, depth average # default: all
+ subsection Depth average
+ set Time between graphical output = 1e6 # default: 1e8
+ end
+ subsection Tracers
+ set Data output format = none
+ set Number of tracers = 1e3
+ set Time between data output = 1e8
+ end
+ subsection Visualization
+ set List of output variables =
+ set Number of grouped files = 0
+ set Output format = vtu
+ set Time between graphical output = 1e6 # default: 1e8
+ end
+end
Modified: trunk/aspect/cookbooks/platelike-boundary.prm
===================================================================
--- trunk/aspect/cookbooks/platelike-boundary.prm 2014-02-17 18:40:09 UTC (rev 2305)
+++ trunk/aspect/cookbooks/platelike-boundary.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -1,3 +1,8 @@
+# A description of convection in a rectangular box where we prescribe
+# temporally variable boundary conditions for the velocity along the top
+# boundary. See the manual for more information.
+
+
############### Global parameters
set Dimension = 2
Added: trunk/aspect/cookbooks/shell_simple_2d.prm
===================================================================
--- trunk/aspect/cookbooks/shell_simple_2d.prm (rev 0)
+++ trunk/aspect/cookbooks/shell_simple_2d.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -0,0 +1,363 @@
+# Listing of Parameters
+# ---------------------
+# In computations, the time step $k$ is chosen according to $k = c \min_K
+# rac{h_K}{\|u\|_{\infty,K} p_T}$ where $h_K$ is the diameter of cell $K$,
+# and the denominator is the maximal magnitude of the velocity on cell $K$
+# times the polynomial degree $p_T$ of the temperature discretization. The
+# dimensionless constant $c$ is called the CFL number in this program. For
+# time discretizations that have explicit components, $c$ must be less than a
+# constant that depends on the details of the time discretization and that is
+# no larger than one. On the other hand, for implicit discretizations such as
+# the one chosen here, one can choose the time step as large as one wants (in
+# particular, one can choose $c>1$) though a CFL number significantly larger
+# than one will yield rather diffusive solutions. Units: None.
+set CFL number = 1.0
+
+# The end time of the simulation. Units: years if the 'Use years in output
+# instead of seconds' parameter is set; seconds otherwise.
+set End time = 1e12
+
+# The name of the directory into which all output files should be placed. This
+# may be an absolute or a relative path.
+set Output directory = output
+
+# A flag indicating whether the computation should be resumed from a
+# previously saved state (if true) or start from scratch (if false).
+set Resume computation = false
+
+# The start time of the simulation. Units: years if the 'Use years in output
+# instead of seconds' parameter is set; seconds otherwise.
+set Start time = 0
+
+# When computing results for mantle convection simulations, it is often
+# difficult to judge the order of magnitude of results when they are stated in
+# MKS units involving seconds. Rather, some kinds of results such as
+# velocities are often stated in terms of meters per year (or, sometimes,
+# centimeters per year). On the other hand, for non-dimensional computations,
+# one wants results in their natural unit system as used inside the code. If
+# this flag is set to 'true' conversion to years happens; if it is 'false', no
+# such conversion happens.
+set Use years in output instead of seconds = true
+
+
+subsection Boundary temperature model
+ # Select one of the following models:
+ #
+ # `spherical constant': A model in
+ # which the temperature is chosen constant on the inner and outer boundaries
+ # of a spherical shell. Parameters are read from subsection 'Sherical
+ # constant'.
+ #
+ # `box': A model in which the temperature is chosen constant on
+ # the left and right sides of a box.
+ set Model name = spherical constant
+
+
+ subsection Spherical constant
+ # Temperature at the inner boundary (core mantle boundary). Units: K.
+ set Inner temperature = 4273
+
+ # Temperature at the outer boundary (lithosphere water/air). Units: K.
+ set Outer temperature = 973
+ end
+
+end
+
+
+subsection Discretization
+ # The polynomial degree to use for the velocity variables in the Stokes
+ # system. Units: None.
+ set Stokes velocity polynomial degree = 2
+
+ # The polynomial degree to use for the temperature variable. Units: None.
+ set Temperature polynomial degree = 2
+
+ # Whether to use a Stokes discretization that is locally conservative at the
+ # expense of a larger number of degrees of freedom (true), or to go with a
+ # cheaper discretization that does not locally conserve mass, although it is
+ # globally conservative (false).
+ set Use locally conservative discretization = false
+
+
+ subsection Stabilization parameters
+ # The exponent $lpha$ in the entropy viscosity stabilization. Units:
+ # None.
+ set alpha = 2
+
+ # The $eta$ factor in the artificial viscosity stabilization. An
+ # appropriate value for 2d is 0.052 and 0.078 for 3d. Units: None.
+ set beta = 0.078
+
+ # The $c_R$ factor in the entropy viscosity stabilization. Units: None.
+ set cR = 0.11
+ end
+
+end
+
+
+subsection Geometry model
+ # Select one of the following models:
+ #
+ # `spherical shell': A geometry
+ # representing a spherical shell or a pice of it. Inner and outer radii are
+ # read from the parameter file in subsection 'Spherical shell'.
+ #
+ # `box': A
+ # box geometry parallel to the coordinate directions. The extent of the box
+ # in each coordinate direction is set in the parameter file.
+ set Model name = spherical shell
+
+
+
+ subsection Spherical shell
+ # Inner radius of the spherical shell. Units: m.
+ set Inner radius = 3481000
+
+ # Opening angle in degrees of the section of the shell that we want to
+ # build. Units: degrees.
+ set Opening angle = 90
+
+ # Outer radius of the spherical shell. Units: m.
+ set Outer radius = 6336000
+ end
+
+end
+
+
+subsection Gravity model
+ # Select one of the following models:
+ #
+ # `vertical': A gravity model in which
+ # the gravity direction is vertically downward and at constant
+ # magnitude.
+ #
+ # `radial constant': A gravity model in which the gravity
+ # direction is radially inward and at constant magnitude. The magnitude is
+ # read from the parameter file in subsection 'Radial constant'.
+ #
+ # `radial earth-like': A gravity model in which the gravity direction is radially
+ # inward and with a magnitude that matches that of the earth at the
+ # core-mantle boundary as well as at the surface and in between is
+ # physically correct under the assumption of a constant density.
+ set Model name = radial earth-like
+
+
+ subsection Radial constant
+ # Magnitude of the gravity vector in $m/s^2$. The direction is always
+ # radially outward from the center of the earth.
+ set Magnitude = 9.81
+ end
+
+end
+
+
+subsection Initial conditions
+ # Select one of the following models:
+ #
+ # `spherical hexagonal perturbation':
+ # An initial temperature field in which the temperature is perturbed
+ # following a six-fold pattern in angular direction from an otherwise
+ # spherically symmetric state.
+ #
+ # `spherical gaussian perturbation': An
+ # initial temperature field in which the temperature is perturbed by a
+ # single Gaussian added to an otherwise spherically symmetric state.
+ # Additional parameters are read from the parameter file in subsection
+ # 'Spherical gaussian perturbation'.
+ #
+ # `perturbed box': An initial
+ # temperature field in which the temperature is perturbed slightly from an
+ # otherwise constant value equal to one. The perturbation is chosen in such
+ # a way that the initial temperature is constant to one along the entire
+ # boundary.
+ set Model name = spherical hexagonal perturbation
+
+
+ subsection Spherical gaussian perturbation
+ # The amplitude of the perturbation.
+ set Amplitude = 0.01
+
+ # The angle where the center of the perturbation is placed.
+ set Angle = 0e0
+
+ # The non-dimensional radial distance where the center of the perturbation
+ # is placed.
+ set Non-dimensional depth = 0.7
+
+ # The standard deviation of the Gaussian perturbation.
+ set Sigma = 0.2
+
+ # The sign of the perturbation.
+ set Sign = 1
+ end
+
+end
+
+
+subsection Material model
+ # Select one of the following models:
+ #
+ # `table': A material model that reads
+ # tables of pressure and temperature dependent material coefficients from
+ # files.
+ #
+ # `Steinberger': lookup from the paper of
+ # Steinberger/Calderwood
+ #
+ # `simple': A simple material model that has
+ # constant values for all coefficients but the density. This model uses the
+ # formulation that assumes an incompressible medium despite the fact that
+ # the density follows the law $
ho(T)=
ho_0(1-eta(T-T_{ ext{ref}})$.
+ # The value for the components of this formula and additional parameters are
+ # read from the parameter file in subsection 'Simple model'.
+ set Model name = simple
+
+
+ subsection Simple model
+ # Reference density $
ho_0$. Units: $kg/m^3$.
+ set Reference density = 3300
+
+ # The reference temperature $T_0$. Units: $K$.
+ set Reference temperature = 293
+
+ # The value of the thermal conductivity $k$. Units: $W/m/K$.
+ set Thermal conductivity = 4.7#1e-6
+
+ # The value of the thermal expansion coefficient $eta$. Units: $1/K$.
+ set Thermal expansion coefficient = 4e-5
+
+ # The value of the constant viscosity. Units: $kg/m/s$.
+ set Viscosity = 1e22
+ end
+
+
+end
+
+
+subsection Mesh refinement
+ # A list of times so that if the end time of a time step is beyond this
+ # time, an additional round of mesh refinement is triggered. This is mostly
+ # useful to make sure we can get through the initial transient phase of a
+ # simulation on a relatively coarse mesh, and then refine again when we are
+ # in a time range that we are interested in and where we would like to use a
+ # finer mesh. Units: each element of the list has units years if the 'Use
+ # years in output instead of seconds' parameter is set; seconds otherwise.
+ set Additional refinement times =
+
+
+ # The number of adaptive refinement steps performed after initial global
+ # refinement but while still within the first time step.
+ set Initial adaptive refinement = 4
+
+ # The number of global refinement steps performed on the initial coarse
+ # mesh, before the problem is first solved there.
+ set Initial global refinement = 5
+
+ # The fraction of cells with the largest error that should be flagged for
+ # refinement.
+ set Refinement fraction = 0.3
+
+ # The fraction of cells with the smallest error that should be flagged for
+ # coarsening.
+ set Coarsening fraction = 0.05
+
+ # The method used to determine which cells to refine and which to coarsen.
+ set Strategy = temperature
+
+ # The number of time steps after which the mesh is to be adapted again based
+ # on computed error indicators.
+ set Time steps between mesh refinement = 15
+end
+
+
+subsection Model settings
+ # A comma separated list of integers denoting those boundaries on which the
+ # temperature is fixed and described by the boundary temperature object
+ # selected in its own section of this input file. All boundary indicators
+ # used by the geometry but not explicitly listed here will end up with
+ # no-flux (insulating) boundary conditions.
+ set Fixed temperature boundary indicators = 0,1
+
+ # Whether to include shear heating into the model or not. From a physical
+ # viewpoint, shear heating should always be used but may be undesirable when
+ # comparing results with known benchmarks that do not include this term in
+ # the temperature equation.
+ set Include shear heating = true
+
+ # A comma separated list of integers denoting those boundaries on which the
+ # velocity is tangential but prescribed, i.e., where external forces act to
+ # prescribe a particular velocity. This is often used to prescribe a
+ # velocity that equals that of overlying plates.
+ set Prescribed velocity boundary indicators =
+
+ # H0
+ set Radiogenic heating rate = 0e0
+
+ # A comma separated list of integers denoting those boundaries on which the
+ # velocity is tangential and unrestrained, i.e., where no external forces
+ # act to prescribe a particular tangential velocity (although there is a
+ # force that requires the flow to be tangential).
+ set Tangential velocity boundary indicators = 1,2,3
+
+ # A comma separated list of integers denoting those boundaries on which the
+ # velocity is zero.
+ set Zero velocity boundary indicators = 0
+end
+
+
+subsection Postprocess
+ # A comma separated list of postprocessor objects that should be run at the
+ # end of each time step. Some of these postprocessors will declare their own
+ # parameters which may, for example, include that they will actually do
+ # something only every so many time steps or years. Alternatively, the text
+ # 'all' indicates that all available postprocessors should be run after each
+ # time step.
+ #
+ # The following postprocessors are available:
+ #
+ # `visualization':
+ # A postprocessor that takes the solution and writes it into files that can
+ # be read by a graphical visualization program. Additional run time
+ # parameters are read from the parameter subsection
+ # 'Visualization'.
+ #
+ # `velocity statistics': A postprocessor that computes
+ # some statistics about the velocity field.
+ #
+ # `temperature statistics': A
+ # postprocessor that computes some statistics about the temperature
+ # field.
+ #
+ # `velocity statistics for the table model': A postprocessor that
+ # computes some statistics about the velocity field.
+ #
+ # `heat flux statistics
+ # for the table model': A postprocessor that computes some statistics about
+ # the heat flux across boundaries.
+ #
+ # `heat flux statistics': A postprocessor
+ # that computes some statistics about the heat flux across boundaries.
+ set List of postprocessors = visualization,velocity statistics,temperature statistics,heat flux statistics, depth average
+
+
+ subsection Visualization
+
+ set Number of grouped files = 0
+
+ # The file format to be used for graphical output.
+ set Output format = vtu
+
+ # The time interval between each generation of graphical output files. A
+ # value of zero indicates that output should be generated in each time
+ # step. Units: years if the 'Use years in output instead of seconds'
+ # parameter is set; seconds otherwise.
+ set Time between graphical output = 1.5e6
+ end
+
+ subsection Depth average
+ set Time between graphical output = 1e6
+ end
+
+end
+
+
Added: trunk/aspect/cookbooks/shell_simple_3d.prm
===================================================================
--- trunk/aspect/cookbooks/shell_simple_3d.prm (rev 0)
+++ trunk/aspect/cookbooks/shell_simple_3d.prm 2014-02-17 19:16:21 UTC (rev 2306)
@@ -0,0 +1,367 @@
+set Dimension = 3
+
+# Listing of Parameters
+# ---------------------
+# In computations, the time step $k$ is chosen according to $k = c \min_K
+# rac{h_K}{\|u\|_{\infty,K} p_T}$ where $h_K$ is the diameter of cell $K$,
+# and the denominator is the maximal magnitude of the velocity on cell $K$
+# times the polynomial degree $p_T$ of the temperature discretization. The
+# dimensionless constant $c$ is called the CFL number in this program. For
+# time discretizations that have explicit components, $c$ must be less than a
+# constant that depends on the details of the time discretization and that is
+# no larger than one. On the other hand, for implicit discretizations such as
+# the one chosen here, one can choose the time step as large as one wants (in
+# particular, one can choose $c>1$) though a CFL number significantly larger
+# than one will yield rather diffusive solutions. Units: None.
+set CFL number = 1.0
+
+# The end time of the simulation. Units: years if the 'Use years in output
+# instead of seconds' parameter is set; seconds otherwise.
+set End time = 1e12
+
+# The name of the directory into which all output files should be placed. This
+# may be an absolute or a relative path.
+set Output directory = /data/bangerth/3d-shell/output
+
+# A flag indicating whether the computation should be resumed from a
+# previously saved state (if true) or start from scratch (if false).
+set Resume computation = true
+
+# The start time of the simulation. Units: years if the 'Use years in output
+# instead of seconds' parameter is set; seconds otherwise.
+set Start time = 0
+
+# When computing results for mantle convection simulations, it is often
+# difficult to judge the order of magnitude of results when they are stated in
+# MKS units involving seconds. Rather, some kinds of results such as
+# velocities are often stated in terms of meters per year (or, sometimes,
+# centimeters per year). On the other hand, for non-dimensional computations,
+# one wants results in their natural unit system as used inside the code. If
+# this flag is set to 'true' conversion to years happens; if it is 'false', no
+# such conversion happens.
+set Use years in output instead of seconds = true
+
+
+subsection Boundary temperature model
+ # Select one of the following models:
+ #
+ # `spherical constant': A model in
+ # which the temperature is chosen constant on the inner and outer boundaries
+ # of a spherical shell. Parameters are read from subsection 'Sherical
+ # constant'.
+ #
+ # `box': A model in which the temperature is chosen constant on
+ # the left and right sides of a box.
+ set Model name = spherical constant
+
+
+ subsection Spherical constant
+ # Temperature at the inner boundary (core mantle boundary). Units: K.
+ set Inner temperature = 4273
+
+ # Temperature at the outer boundary (lithosphere water/air). Units: K.
+ set Outer temperature = 973
+ end
+
+end
+
+
+subsection Discretization
+ # The polynomial degree to use for the velocity variables in the Stokes
+ # system. Units: None.
+ set Stokes velocity polynomial degree = 2
+
+ # The polynomial degree to use for the temperature variable. Units: None.
+ set Temperature polynomial degree = 2
+
+ # Whether to use a Stokes discretization that is locally conservative at the
+ # expense of a larger number of degrees of freedom (true), or to go with a
+ # cheaper discretization that does not locally conserve mass, although it is
+ # globally conservative (false).
+ set Use locally conservative discretization = false
+
+
+ subsection Stabilization parameters
+ # The exponent $lpha$ in the entropy viscosity stabilization. Units:
+ # None.
+ set alpha = 2
+
+ # The $eta$ factor in the artificial viscosity stabilization. An
+ # appropriate value for 2d is 0.052 and 0.078 for 3d. Units: None.
+ set beta = 0.078
+
+ # The $c_R$ factor in the entropy viscosity stabilization. Units: None.
+ set cR = 0.11
+ end
+
+end
+
+
+subsection Geometry model
+ # Select one of the following models:
+ #
+ # `spherical shell': A geometry
+ # representing a spherical shell or a pice of it. Inner and outer radii are
+ # read from the parameter file in subsection 'Spherical shell'.
+ #
+ # `box': A
+ # box geometry parallel to the coordinate directions. The extent of the box
+ # in each coordinate direction is set in the parameter file.
+ set Model name = spherical shell
+
+
+
+ subsection Spherical shell
+ # Inner radius of the spherical shell. Units: m.
+ set Inner radius = 3481000
+
+ # Outer radius of the spherical shell. Units: m.
+ set Outer radius = 6336000
+ end
+
+end
+
+
+subsection Gravity model
+ # Select one of the following models:
+ #
+ # `vertical': A gravity model in which
+ # the gravity direction is vertically downward and at constant
+ # magnitude.
+ #
+ # `radial constant': A gravity model in which the gravity
+ # direction is radially inward and at constant magnitude. The magnitude is
+ # read from the parameter file in subsection 'Radial constant'.
+ #
+ # `radial earth-like': A gravity model in which the gravity direction is radially
+ # inward and with a magnitude that matches that of the earth at the
+ # core-mantle boundary as well as at the surface and in between is
+ # physically correct under the assumption of a constant density.
+ set Model name = radial earth-like
+
+
+ subsection Radial constant
+ # Magnitude of the gravity vector in $m/s^2$. The direction is always
+ # radially outward from the center of the earth.
+ set Magnitude = 9.81
+ end
+
+end
+
+
+subsection Initial conditions
+ # Select one of the following models:
+ #
+ # `spherical hexagonal perturbation':
+ # An initial temperature field in which the temperature is perturbed
+ # following a six-fold pattern in angular direction from an otherwise
+ # spherically symmetric state.
+ #
+ # `spherical gaussian perturbation': An
+ # initial temperature field in which the temperature is perturbed by a
+ # single Gaussian added to an otherwise spherically symmetric state.
+ # Additional parameters are read from the parameter file in subsection
+ # 'Spherical gaussian perturbation'.
+ #
+ # `perturbed box': An initial
+ # temperature field in which the temperature is perturbed slightly from an
+ # otherwise constant value equal to one. The perturbation is chosen in such
+ # a way that the initial temperature is constant to one along the entire
+ # boundary.
+ set Model name = spherical hexagonal perturbation
+
+
+ subsection Spherical gaussian perturbation
+ # The amplitude of the perturbation.
+ set Amplitude = 0.01
+
+ # The angle where the center of the perturbation is placed.
+ set Angle = 0e0
+
+ # The non-dimensional radial distance where the center of the perturbation
+ # is placed.
+ set Non-dimensional depth = 0.7
+
+ # The standard deviation of the Gaussian perturbation.
+ set Sigma = 0.2
+
+ # The sign of the perturbation.
+ set Sign = 1
+ end
+
+end
+
+
+subsection Material model
+ # Select one of the following models:
+ #
+ # `table': A material model that reads
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