[cig-commits] commit 2511 by heister to /var/svn/dealii/aspect
dealii.demon at gmail.com
dealii.demon at gmail.com
Sun Apr 13 08:02:05 PDT 2014
Revision 2511
formatting and rewrapping
U trunk/aspect/doc/modules/0.1-to-0.2.h
U trunk/aspect/doc/modules/0.2-to-0.3.h
U trunk/aspect/doc/modules/changes.h
U trunk/aspect/doc/modules/todo.h
http://www.dealii.org/websvn/revision.php?repname=Aspect+Repository&path=%2F&rev=2511&peg=2511
Diff:
Modified: trunk/aspect/doc/modules/0.1-to-0.2.h
===================================================================
--- trunk/aspect/doc/modules/0.1-to-0.2.h 2014-04-13 15:01:11 UTC (rev 2510)
+++ trunk/aspect/doc/modules/0.1-to-0.2.h 2014-04-13 15:02:02 UTC (rev 2511)
@@ -1,314 +1,265 @@
/**
- * @page changes_between_0.1_and_0.2 Changes between version 0.1 and version 0.2
- *
- * <p>
- * This is the list of changes made after the release of
- * Aspect version 0.1 and before 0.2.
- * All entries are signed with the names of the author.
+ * @page changes_between_0.1_and_0.2 Changes between version 0.1 and version
+ * 0.2
+ *
+ * <p> This is the list of changes made after the release of Aspect version
+ * 0.1 and before 0.2. All entries are signed with the names of the author.
* </p>
- *
+ *
* <ol>
- * <li>
- * Changed: Some models declared parameters that indicate the names of
- * files and that contained underscores. These have been renamed to
- * contain dashes instead, to avoid perpetual difficulties in creating
- * the manual.
+ * <li> Changed: Some models declared parameters that indicate the names of
+ * files and that contained underscores. These have been renamed to contain
+ * dashes instead, to avoid perpetual difficulties in creating the manual.
* <br>
* (Timo Heister, 2013/04/28)
- *
- * <li>
- * Fixed: cleanup the various depth_average functions. Fix that
- * all quantities got averaged the wrong way if the mesh was
- * adaptively refined. Additionally, the velocity_magnitude
- * and sinking_velocity was computed incorrectly.
+ *
+ * <li> Fixed: cleanup the various depth_average functions. Fix that all
+ * quantities got averaged the wrong way if the mesh was adaptively refined.
+ * Additionally, the velocity_magnitude and sinking_velocity was computed
+ * incorrectly.
* <br>
* (Timo Heister, 2013/04/28)
- *
- * <li>
- * Fixed: Writing in any output format other than VTU and HDF5 did not
+ *
+ * <li> Fixed: Writing in any output format other than VTU and HDF5 did not
* yield any output files. This is now fixed.
* <br>
* (Wolfgang Bangerth, 2013/04/28)
- *
- * <li>
- * Fixed: There were many places where we indiscriminately used MPI_COMM_WORLD,
- * rather than the communicator used for the actual simulation. This is not a
- * problem almost all the time, except for cases where Aspect is run as part
- * of a bigger simulation.
+ *
+ * <li> Fixed: There were many places where we indiscriminately used
+ * MPI_COMM_WORLD, rather than the communicator used for the actual
+ * simulation. This is not a problem almost all the time, except for cases
+ * where Aspect is run as part of a bigger simulation.
* <br>
* (Wolfgang Bangerth, 2013/04/28)
- *
- * <li>
- * New: All parts of the code now use the new MaterialModel::evaluate().
- * The individual functions like viscosity() got removed. To get an
- * old material model to work, you can either move to the new setup
- * or derive from InterfaceCompatibility instead of Interface.
+ *
+ * <li> New: All parts of the code now use the new MaterialModel::evaluate().
+ * The individual functions like viscosity() got removed. To get an old
+ * material model to work, you can either move to the new setup or derive from
+ * InterfaceCompatibility instead of Interface.
* <br>
* (Timo Heister, 2013/04/28)
- *
- * <li>
- * New: Checking whether the end time has been reached is now a regular
- * termination criterion plugin. Unlike other plugins, however, it is
- * always active.
+ *
+ * <li> New: Checking whether the end time has been reached is now a regular
+ * termination criterion plugin. Unlike other plugins, however, it is always
+ * active.
* <br>
* (Wolfgang Bangerth, 2013/04/28)
- *
- * <li>
- * New: The following plugin subsystems are now documented: mesh refinement
- * criteria, termination criteria, and velocity boundary conditions.
+ *
+ * <li> New: The following plugin subsystems are now documented: mesh
+ * refinement criteria, termination criteria, and velocity boundary
+ * conditions.
* <br>
* (Wolfgang Bangerth, 2013/04/28)
- *
- * <li>
- * New: There is now a new top-level parameter, "Number of cheap Stokes
- * solver steps" that allows choosing how many iterations the Stokes
- * solver should attempt using the "cheap" preconditioner described in
- * the ASPECT paper. In particular, a value of zero indicates that the
- * first phase should be skipped altogether. This is a useful strategy for
- * problems with strongly varying viscosity for which the cheap preconditioner
- * does not help very much and the time used for this first phase is often
- * wasted.
+ *
+ * <li> New: There is now a new top-level parameter, "Number of cheap Stokes
+ * solver steps" that allows choosing how many iterations the Stokes solver
+ * should attempt using the "cheap" preconditioner described in the ASPECT
+ * paper. In particular, a value of zero indicates that the first phase should
+ * be skipped altogether. This is a useful strategy for problems with strongly
+ * varying viscosity for which the cheap preconditioner does not help very
+ * much and the time used for this first phase is often wasted.
* <br>
* (Wolfgang Bangerth, 2013/04/22)
- *
- * <li>
- * Fixed: Entropy exponent stabilization_alpha ("alpha") should be an
- * integer, not a double. The recommended setting is the value 2.
- * Note that the value 1 is not explained in the ASPECT paper, only
- * a value of 2. The various other stabilization parameters have also
- * been better explained and cross-referenced to the ASPECT paper.
+ *
+ * <li> Fixed: Entropy exponent stabilization_alpha ("alpha") should be an
+ * integer, not a double. The recommended setting is the value 2. Note that
+ * the value 1 is not explained in the ASPECT paper, only a value of 2. The
+ * various other stabilization parameters have also been better explained and
+ * cross-referenced to the ASPECT paper.
* <br>
* (Timo Heister, 2013/04/17)
- *
- * <li>
- * Fixed: When running an input file that simply forgot to provide
- * names to certain plugins (for example, that does not list anything
- * at all for the geometry model), the resulting error message was
- * pretty obscure and non-informative. This has now been fixed: the
- * error message is much more descriptive and at least says where the
- * error may have happened and what the missing parameter is.
+ *
+ * <li> Fixed: When running an input file that simply forgot to provide names
+ * to certain plugins (for example, that does not list anything at all for the
+ * geometry model), the resulting error message was pretty obscure and non-
+ * informative. This has now been fixed: the error message is much more
+ * descriptive and at least says where the error may have happened and what
+ * the missing parameter is.
* <br>
* (Wolfgang Bangerth, 2013/04/05)
- *
- * <li>
- * New: A postprocessor to output the sparsity pattern of the block
+ *
+ * <li> New: A postprocessor to output the sparsity pattern of the block
* matrix. Intended mainly for debugging purposes.
* <br>
* (Ted Studley, 2012/12/21)
- *
- * <li>
- * New: a module for specifying termination criteria has been
- * added. The first termination criteria is detecting steady
- * state RMS velocity. This scheme also allows checkpointing
- * the simulation right before termination.
+ *
+ * <li> New: a module for specifying termination criteria has been added. The
+ * first termination criteria is detecting steady state RMS velocity. This
+ * scheme also allows checkpointing the simulation right before termination.
* <br>
* (Eric Heien, 2012/12/11)
- *
- * <li>
- * New: The way we do mesh refinement has been completely rewritten.
- * This is now handled via plugins that provide different
- * refinement strategies and that can be combined if
- * so desired. The names of refinement criteria have also been
- * changed: "Temperature", "Velocity", and "Density c_p temperature"
+ *
+ * <li> New: The way we do mesh refinement has been completely rewritten. This
+ * is now handled via plugins that provide different refinement strategies and
+ * that can be combined if so desired. The names of refinement criteria have
+ * also been changed: "Temperature", "Velocity", and "Density c_p temperature"
* have been renamed to "temperature", "velocity", and "thermal energy
- * density". Furthermore, the effect of the old name "Normalized density
- * and temperature" can be obtained by passing the list
- * "density, temperature". For more detail, see the manual's section
- * on parameters that describe the mesh refinement process.
+ * density". Furthermore, the effect of the old name "Normalized density and
+ * temperature" can be obtained by passing the list "density, temperature".
+ * For more detail, see the manual's section on parameters that describe the
+ * mesh refinement process.
* <br>
* (Wolfgang Bangerth, 2012/12/08)
- *
- * <li>
- * Fixed: In nonlinear models, we did not recompute the matrix and
- * preconditioner for the Stokes system in every time step. This is
- * now fixed.
+ *
+ * <li> Fixed: In nonlinear models, we did not recompute the matrix and
+ * preconditioner for the Stokes system in every time step. This is now fixed.
* <br>
* (Wolfgang Bangerth, 2012/12/04)
- *
- * <li>
- * Changed: Write the parameter file only on the root node
- * to avoid file system locking issues.
+ *
+ * <li> Changed: Write the parameter file only on the root node to avoid file
+ * system locking issues.
* <br>
* (Eric Heien, 2012/11/28)
- *
- * <li>
- * Changed: Adjusted the stabilization parameters to stabilize
- * advection benchmarks without natural diffusion.
+ *
+ * <li> Changed: Adjusted the stabilization parameters to stabilize advection
+ * benchmarks without natural diffusion.
* <br>
* (Rene Gassmoeller, 2012/11/16)
- *
- * <li>
- * Changed: Unified the routines for advecting temperature and
- * compositional fields. This includes a different scaling for
- * the temperature stabilization that may change results.
+ *
+ * <li> Changed: Unified the routines for advecting temperature and
+ * compositional fields. This includes a different scaling for the temperature
+ * stabilization that may change results.
* <br>
* (Rene Gassmoeller, 2012/11/15)
- *
- * <li>
- * New: If the "Use conduction timestep" parameter is true, the timestep
+ *
+ * <li> New: If the "Use conduction timestep" parameter is true, the timestep
* is calculated as the minimum of the convection *and* heat conduction
- * timesteps. This is to allow models where flow is very slow relative
- * to conduction.
+ * timesteps. This is to allow models where flow is very slow relative to
+ * conduction.
* <br>
* (Eric Heien, 2012/11/06)
- *
- * <li>
- * New: Aspect now catches if the output directory specified in
- * the parameter file does not exist, rather than providing a
- * cryptic error message upon first attempt to write to this
- * directory.
+ *
+ * <li> New: Aspect now catches if the output directory specified in the
+ * parameter file does not exist, rather than providing a cryptic error
+ * message upon first attempt to write to this directory.
* <br>
* (Wolfgang Bangerth, 2012/10/21)
- *
- * <li>
- * New: Material models can now depend on compositional fields.
+ *
+ * <li> New: Material models can now depend on compositional fields.
* <br>
* (Juliane Dannberg, 2012/10/19)
- *
- * <li>
- * New: Introduce compositional fields, that are advected by the velocity.
+ *
+ * <li> New: Introduce compositional fields, that are advected by the
+ * velocity.
* <br>
* (Juliane Dannberg, 2012/10/19)
- *
- * <li>
- * New: There is now a plugin that allows using GPlates velocity models
+ *
+ * <li> New: There is now a plugin that allows using GPlates velocity models
* as input for the velocity boundary conditions.
* <br>
* (Rene Gassmoeller, 2012/10/18)
- *
- * <li>
- * Changed: SimulatorAccess moved from aspect::Postproccessor to aspect:: and
- * can be used in material/gravity/... models too. If needed, derive from SimulatorAccess.
+ *
+ * <li> Changed: SimulatorAccess moved from aspect::Postproccessor to aspect::
+ * and can be used in material/gravity/... models too. If needed, derive from
+ * SimulatorAccess.
* <br>
* (Timo Heister, 2012/09/24)
- *
- * <li>
- * Fixed: Resume does no longer trigger additional refinement times in the past.
+ *
+ * <li> Fixed: Resume does no longer trigger additional refinement times in
+ * the past.
* <br>
* (Timo Heister, 2012/09/20)
- *
- * <li>
- * New: Add structures for iterated IMPES and nonlinear solvers.
+ *
+ * <li> New: Add structures for iterated IMPES and nonlinear solvers.
* <br>
* (Markus Buerg, 2012/09/20)
- *
- * <li>
- * New: InitialCondition::Function for the temperature given in the parameter
- * file.
+ *
+ * <li> New: InitialCondition::Function for the temperature given in the
+ * parameter file.
* <br>
* (Timo Heister, 2012/09/17)
- *
- * <li>
- * New: BoundaryTemperature::Box is more flexible because it has parameters
- * for the values for all sides of the box.
+ *
+ * <li> New: BoundaryTemperature::Box is more flexible because it has
+ * parameters for the values for all sides of the box.
* <br>
* (Timo Heister, 2012/09/17)
- *
- * <li>
- * New: Added parameter 'Temperature solver tolerance' to control the
+ *
+ * <li> New: Added parameter 'Temperature solver tolerance' to control the
* accuracy of the temperature solver.
* <br>
* (Timo Heister, 2012/09/05)
- *
- * <li>
- * New: Added MaterialModel::update() and GravityModel::update() that are
+ *
+ * <li> New: Added MaterialModel::update() and GravityModel::update() that are
* called before every time step.
* <br>
* (Timo Heister, 2012/09/05)
- *
- * <li>
- * New: Support for HDF5/XDMF visualization output.
+ *
+ * <li> New: Support for HDF5/XDMF visualization output.
* <br>
* (Eric Heien, 2012/08/28)
- *
- * <li>
- * New: It is now possible to select the tolerance for linear
- * solvers from the parameter file via the global parameter
- * "Linear solver tolerance".
+ *
+ * <li> New: It is now possible to select the tolerance for linear solvers
+ * from the parameter file via the global parameter "Linear solver tolerance".
* <br>
* (Wolfgang Bangerth, 2012/06/30)
- *
- * <li>
- * New: Tracer particle postprocesser can write in parallel to HDF5.
+ *
+ * <li> New: Tracer particle postprocesser can write in parallel to HDF5.
* <br>
* (Eric Heien, 2012/06/08)
- *
- * <li>
- * New: Tracer particle postprocessor also outputs
- * <code>particle.pvd</code> for ParaView. Tracer particle data may
- * also be output to ASCII files for easy parsing and analysis.
+ *
+ * <li> New: Tracer particle postprocessor also outputs
+ * <code>particle.pvd</code> for ParaView. Tracer particle data may also be
+ * output to ASCII files for easy parsing and analysis.
* <br>
* (Eric Heien, 2012/06/01)
- *
- * <li>
- * New: Aspect now writes a <code>solution.pvd</code> for Paraview
- * that contains a list of the files that jointly make up the entire
- * simulation (and not just a single time step) together with the
- * simulation time each of the files that describe a time step correspond
- * to.
+ *
+ * <li> New: Aspect now writes a <code>solution.pvd</code> for Paraview that
+ * contains a list of the files that jointly make up the entire simulation
+ * (and not just a single time step) together with the simulation time each of
+ * the files that describe a time step correspond to.
* <br>
* (Wolfgang Bangerth, 2012/05/30)
- *
- * <li>
- * New: It is now selectable how the pressure should be normalized
- * (and if it should be normalized at all). If it should be normalized
- * at the end of each time step, one can select if the average
- * pressure at the top surface, or the average pressure throughout the
- * entire domain should be set to a given value (for example to zero).
+ *
+ * <li> New: It is now selectable how the pressure should be normalized (and
+ * if it should be normalized at all). If it should be normalized at the end
+ * of each time step, one can select if the average pressure at the top
+ * surface, or the average pressure throughout the entire domain should be set
+ * to a given value (for example to zero).
* <br>
* (Wolfgang Bangerth, 2012/05/15)
- *
- * <li>
- * New: The variables we output in graphical format files are now
- * user selectable from the input parameter file. Functions that
- * compute something from velocity, pressure and temperature (e.g.,
- * the viscosity, strain rate, etc) are now implemented as plugins
- * like many of the other parts of Aspect.
+ *
+ * <li> New: The variables we output in graphical format files are now user
+ * selectable from the input parameter file. Functions that compute something
+ * from velocity, pressure and temperature (e.g., the viscosity, strain rate,
+ * etc) are now implemented as plugins like many of the other parts of Aspect.
* now implemented
* <br>
* (Wolfgang Bangerth, 2012/05/08)
- *
- * <li>
- * Modified: Checkpoint frequency is now a user specified parameter.
+ *
+ * <li> Modified: Checkpoint frequency is now a user specified parameter.
* Frequency may be specified as either wall time or number of time steps.
* <br>
* (Eric Heien, 2012/05/04)
- *
- * <li>
- * Modified: Background writing of visualization data now uses the
- * mkstemp function rather than forking mktemp, and will continue as
- * normal (at lower efficiency) if temporary files cannot be created.
+ *
+ * <li> Modified: Background writing of visualization data now uses the
+ * mkstemp function rather than forking mktemp, and will continue as normal
+ * (at lower efficiency) if temporary files cannot be created.
* <br>
* (Eric Heien, 2012/05/03)
- *
- * <li>
- * New: The compressibility that functions implementing the interface
+ *
+ * <li> New: The compressibility that functions implementing the interface
* aspect::MaterialModel::Interface::compressibility() need to return was
- * previously defined incorrectly as $ rac{\partial
ho}{\partial p}$.
- * This is not what is commonly referred to as compressibility, and
- * the function is now supposed to return
- * $ rac 1
ho rac{\partial
ho}{\partial p}$ instead, following the
- * common definition of the word.
+ * previously defined incorrectly as $ rac{\partial
ho}{\partial p}$. This
+ * is not what is commonly referred to as compressibility, and the function is
+ * now supposed to return $ rac 1
ho rac{\partial
ho}{\partial p}$
+ * instead, following the common definition of the word.
* <br>
- * Note that all currently implemented compressible models already did
- * that.
+ * Note that all currently implemented compressible models already did that.
* <br>
* (Wolfgang Bangerth, Timo Heister, 2012/05/03)
- *
- * <li>
- * New: The number of space dimensions in which a simulation happens is now
- * a parameter that is set in the input parameter filer, rather than
+ *
+ * <li> New: The number of space dimensions in which a simulation happens is
+ * now a parameter that is set in the input parameter filer, rather than
* statically at compile time as before.
* <br>
* (Wolfgang Bangerth, 2012/04/03)
- *
- * <li>
- * New: A postprocessor module for particles was added. This module creates
- * a random uniform distribution of particles in the mesh and moves them based
- * on the velocity field using an RK2 scheme.
+ *
+ * <li> New: A postprocessor module for particles was added. This module
+ * creates a random uniform distribution of particles in the mesh and moves
+ * them based on the velocity field using an RK2 scheme.
* <br>
* (Eric Heien, 2012/04/02)
* </ol>
- *
- *
+ *
+ *
*/
Modified: trunk/aspect/doc/modules/0.2-to-0.3.h
===================================================================
--- trunk/aspect/doc/modules/0.2-to-0.3.h 2014-04-13 15:01:11 UTC (rev 2510)
+++ trunk/aspect/doc/modules/0.2-to-0.3.h 2014-04-13 15:02:02 UTC (rev 2511)
@@ -1,33 +1,29 @@
/**
- * @page changes_between_0.2_and_0.3 Changes between version 0.2 and version 0.3
- *
- * <p>
- * This is the list of changes made after the release of
- * Aspect version 0.2 and before 0.3.
- * All entries are signed with the names of the author.
+ * @page changes_between_0.2_and_0.3 Changes between version 0.2 and version
+ * 0.3
+ *
+ * <p> This is the list of changes made after the release of Aspect version
+ * 0.2 and before 0.3. All entries are signed with the names of the author.
* </p>
- *
+ *
* <ol>
- * <li>
- * Changed: To unify spelling, the environment variable that indicates
+ * <li> Changed: To unify spelling, the environment variable that indicates
* the directory in which deal.II is located is now called
- * <code>DEAL_II_DIR</code> instead of the old <code>DEAL_DIR</code>. The
- * old spelling is still accepted, however.
+ * <code>DEAL_II_DIR</code> instead of the old <code>DEAL_DIR</code>. The old
+ * spelling is still accepted, however.
* <br>
* (Wolfgang Bangerth, 2013/05/31)
- *
- * <li>
- * Fixed: Fix a bug in adiabatic initial conditions introduced in r1599.
+ *
+ * <li> Fixed: Fix a bug in adiabatic initial conditions introduced in r1599.
* <br>
* (Juliane Dannberg, 2013/05/08)
- *
- * <li>
- * New: The doxygen generated documentation of ASPECT now automatically
+ *
+ * <li> New: The doxygen generated documentation of ASPECT now automatically
* has references to all of the deal.II classes used.
* <br>
* (Wolfgang Bangerth, 2013/05/04)
- *
+ *
* </ol>
- *
- *
+ *
+ *
*/
Modified: trunk/aspect/doc/modules/changes.h
===================================================================
--- trunk/aspect/doc/modules/changes.h 2014-04-13 15:01:11 UTC (rev 2510)
+++ trunk/aspect/doc/modules/changes.h 2014-04-13 15:02:02 UTC (rev 2511)
@@ -1,409 +1,390 @@
/**
* @page changes_after_0_3 Changes after Version 0.3
- *
- * <p>
- * This is the list of changes made after the release of
- * Aspect version 0.3.
- * All entries are signed with the names of the author.
- * </p>
- *
+ *
+ * <p> This is the list of changes made after the release of Aspect version
+ * 0.3. All entries are signed with the names of the author. </p>
+ *
* <ol>
- * <li>New: There is now a cookbook describing the
- * usage of the GPlates plugin and possible applications.
- * The internal velocity representation in the plugin was
- * changed to cartesian and a smoothing algorithm was
- * introduced.
- * <br>
- * (Rene Gassmoeller, Wolfgang Bangerth, 2014/04/12)
- *
- * <li>New: A global parameter ``Maximum time step''
- * allows the user to select the largest time step that
- * a simulation can take. This may be useful for
- * complicated models or benchmarking.
- * <br>
- * (Ian Rose, Wolfgang Bangerth, 2014/04/12)
- *
- * <li>Fixed: The simple material model now ignores negative
- * compositional values that can occur from numerical undershots
- * and even interpolation onto the FE space. This makes the
- * cookbook/composition-active.prm work again.
- * <br>
- * (Timo Heister, 2014/04/08)
- *
- * <li>New: New options to remove rotational/translational modes
- * from the solution.
- * <br>
- * (Ian Rose, Timo Heister, 2014/04/07)
- *
- * <li>New: A geometry model implementing a full sphere. There is also
- * a corresponding gravity model where gravity increases linearly as you
- * move outward.
- * <br>
- * (Ian Rose, 2014/04/07)
- *
- * <li>New: The box geometry allows you to specify a repetition
- * argument in each coordinate direction.
- * <br>
- * (Timo Heister, 2014/04/07)
- *
- * <li>New: On startup, ASPECT now prints out whether it is
- * running in debug or optimized mode. This is now part of a general
- * status message at the top of every run.
- * <br>
- * (Wolfgang Bangerth, Juliane Dannberg, 2014/04/7)
- *
- * <li>Changed: The GPlates plugin for surface velocities always
- * interpreted the start time of the model and the time increment
- * between individual input files in seconds. It now honors the
- * 'Use years in output instead of seconds' flag in the input file.
- * <br>
- * (Wolfgang Bangerth, Rene Gassmoeller, 2014/04/01)
- *
- * <li>New: CMake now passes down a preprocessor defined string constant
- * called <code>ASPECT_SOURCE_DIR</code> that is set to the (top level)
- * directory in which the ASPECT sources are located. This can be used
- * by plugins to locate where data files are (e.g., in the <code>data/</code>
- * directory of the source tree) independent of where the executable is
- * finally called.
- * <br>
- * (Wolfgang Bangerth, 2014/03/31)
- *
- * <li>New: The manual now contains a cookbook section that discussed a
- * model running in a 3d spherical shell. Movies for this model can
- * be found at https://www.youtube.com/channel/UCDTTQ068ablZ8k9J31wNk_Q .
- * <br>
- * (Wolfgang Bangerth 2014/03/30)
- *
- * <li>Changed: The 'radial constant' gravity model had a default of
- * $30 m/s^2$ for the magnitude of the gravity. This value makes no
- * sense. It has therefore been changed to the value we have at
- * Earth's surface: $9.81 m/s^2$.
- * <br>
- * (Wolfgang Bangerth, 2014/03/29)
- *
- * <li>Fixed: Correct computation of min/max composition statistics.
- * <br>
- * (Timo Heister, 2014/03/26)
- *
- * <li>Fixed: Corrected calculation of non-dimensional temperature in the
- * temperature statistics postprocessor plugin.
- * <br>
- * (Eric Heien, 2014/03/24)
- *
- * <li>Fixed: Restarting from a previously checkpointed solution
- * did not work when using the Intel compiler and its standard library.
- * This is now fixed.
- * <br>
- * (Wolfgang Bangerth, Jacqueline Austermann 2014/03/21)
- *
- * <li>New: There is now a postprocessor that computes a measure of
- * dynamic topography, based on the vertical component of the stress.
- * There is also a visualization postprocessor that allows to write this
- * information into the visualization files to generate graphical
- * representations of the data.
- * <br>
- * (Wolfgang Bangerth, Jacqueline Austermann 2014/03/20)
- *
- * <li>New: Aspect now installs a file <code>AspectConfig.cmake</code>
- * into the same directory as the executable that can be used by
- * plugins to set up compiler flags, include paths, etc, to compile
- * a set of source files into a shared library that can then be
- * loaded at run time from the input file. See the manual for more
- * information about this mechanism.
- * <br>
- * (Matthias Maier, Wolfgang Bangerth 2014/03/03)
- *
- * <li>New: The manual now contains a cookbook section introducing a
- * model that runs in a two-dimensional annulus.
- * <br>
- * (Wolfgang Bangerth 2014/02/17)
- *
- * <li>New: When running long simulations, the output generated by
- * the "depth average" postprocessor can become messy and hard
- * to visualize in the format previously used because it was,
- * essentially, just a text based table. The data is now written
- * into a file, named <code>depth_average.ext</code> in the
- * output directory, in any of the output formats supported
- * by deal.II, where <code>ext</code> is the matching file
- * name extension for the format. This allows visualization
- * as a time-depth plot. The format is selected in the input
- * file, along with a number of other settings.
- * <br>
- * (Wolfgang Bangerth 2014/02/16)
- *
- * <li>New: The "depth average" postprocessor now takes a run-time
- * parameter in the "Postprocess/Depth average" section of the input
- * file that specifies into how many depth slices the domain should
- * be subdivided in computing depth averages.
- * <br>
- * (Wolfgang Bangerth 2014/02/14)
- *
- * <li>Fixed: The "depth average" postprocessor did not honor the
- * "Use years in output instead of seconds" parameter in the input
- * file and instead always printed time in seconds when generating
- * output. This is now fixed.
- * <br>
- * (Wolfgang Bangerth 2014/02/11)
- *
- * <li>New: The "Simple setups" section of the manual now has a subsection
- * detailing the generalization of the "Convection in a box" setup to
- * a three-dimensional situation. This includes links to the movies
- * already available http://www.youtube.com/watch?v=_bKqU_P4j48 and
- * http://www.youtube.com/watch?v=CzCKYyR-cmg .
- * <br>
- * (Wolfgang Bangerth 2014/01/29)
- *
- * <li>New: The manual has a new subsection at the top of the "Cookbooks"
- * section providing a bit of an outline of how one sets up situations.
- * <br>
- * (Wolfgang Bangerth 2014/01/29)
- *
- * <li>New: Linear algebra can be done using PETSc instead of Trilinos. For
- * this, deal.II needs to be configured with PETSc and the preprocessor
- * define <code>USE_PETSC</code>
- * needs to be set in the Aspect file <code>include/aspect/global.h</code> before
- * compiling. This feature is still experimental.
- * <br>
- * (Timo Heister, Ian Rose 2014/01/21)
- *
- * <li>Fixed: On systems where one needs to link executables statically
- * (for example on big clusters), it is not possible to load additional
- * plugins via external shared libraries. This is now disabled and any
- * attempt to do so will lead to a run-time error.
- * <br>
- * (Rene Gassmoeller, Wolfgang Bangerth 2014/01/10)
- *
- * <li>New: There is now a section in the manual that describes how to
- * reproduce the van Keken et al. benchmark.
- * <br>
- * (Cedric Thieulot, Juliane Dannberg,
- * Timo Heister, Wolfgang Bangerth 2014/01/10)
- *
- * <li>Fixed: Using the 'density', 'nonadiabatic temperature', 'thermal
- * energy' or 'viscosity' mesh refinement criterion for parallel computations
- * led to meshes that made no sense. This was due to a bug in deal.II, not
- * Aspect, and has been fixed starting with deal.II 8.1. Using this version
- * of deal.II now also fixes the problem in Aspect.
- * <br>
- * (Wolfgang Bangerth 2013/12/18)
- *
- * <li>Fixed: The 'temperature statistics' postprocessor put a column
- * 'Average nondimensional temperature (K)' into the statistics file that
- * was computed as the average temperature divided by the maximal temperature
- * at the boundary. This made no sense if the maximal temperature at the
- * boundary was zero or if the minimal temperature was nonzero. In fact,
- * it also made no sense if the temperature at the boundary was not prescribed.
- * This is now fixed: the column is computed as the ratio of the average temperature
- * divided by the <i>difference</i> between maximal and minimal temperature,
- * and it is omitted altogether if the temperature is not prescribed on any
- * part of the boundary or if the difference between minimal and maximal
- * prescribed boundary is zero.
- * <br>
- * (Wolfgang Bangerth 2013/12/05)
- *
- * <li>New: There is now a run time parameter that indices the minimal
- * refinement level of the mesh.
- * <br>
- * (Juliane Dannberg 2013/12/03)
- *
- * <li>New: The 'composition' mesh refinement criterion now allows to scale
- * the various compositional fields differently, through parameters given
- * in the input file.
- * <br>
- * (Juliane Dannberg 2013/12/03)
- *
- * <li>New: There are now two new mesh refinement criteria: 'nonadiabatic
- * temperature' refines based on the nonadiabatic part of the temperature
- * field; 'viscosity' refines based on the viscosity considered as a spatially
- * variable field.
- * <br>
- * (Juliane Dannberg 2013/12/03)
- *
- * <li>Fixed: When using adiabatic initial conditions with a shell geometry and
- * an opening angle of 90 degrees, the perturbation was not located where it
- * was supposed to be. This is now fixed.
- * <br>
- * (Juliane Dannberg 2013/12/02)
- *
- * <li>New: There are now boundary temperature and boundary composition models
- * that simply use the initial temperature and composition as the values
- * that should hold at the boundary for all future times.
- * <br>
- * (Juliane Dannberg 2013/12/02)
- *
- * <li>New: Material models can now include reactions between compositional
- * species.
- * <br>
- * (Juliane Dannberg 2013/12/01)
- *
- * <li>Fixed: The shear heating term $2\eta \left( arepsilon(\mathbf u)-
- * rac 13 ( extrm{div}\; \mathbf u)I
ight):\left( arepsilon(\mathbf u)-
- * rac 13 ( extrm{div}\; \mathbf u)I
ight)$ was computed wrongly for
- * compressible models for which the divergence of the velocity field is
- * nonzero. This is now fixed.
- * <br>
- * (Wolfgang Bangerth 2013/11/25)
- *
- * <li>Fixed: The composition and temperature statistics postprocessors
- * incorrectly computed the maximal compositional values and maximal
- * temperature if this maximum was less than or equal to zero. This
- * is now fixed.
- * <br>
- * (Wolfgang Bangerth 2013/11/25)
- *
- * <li>New: One can now select in the input file that the model should
- * include latent heat. The generation of latent heat then needs to be
- * described in the material model.
- * <br>
- * (Juliane Dannberg 2013/11/24)
- *
- * <li>New: It is now possible to prescribe boundary values for
- * compositional fields in cases where there is inflow through
- * a segment of the boundary. This is implemented through a set
- * of plugins for boundary values in the same way as is done for
- * temperature boundary values.
- * <br>
- * (Juliane Dannberg 2013/11/24)
- *
- * <li>New: There is now a refinement criterion "topography" that makes sure
- * the mesh is always refined at the surface of the domain.
- * <br>
- * (Juliane Dannberg 2013/11/24)
- *
- * <li>Fixed: When using compressible models with nonlinear iterations
- * such as "Stokes", "iterated IMPES" or "iterated Stokes" and prescribed
- * boundary values, there were numerous bugs that should now be fixed.
- * <br>
- * (Wolfgang Bangerth 2013/11/21)
- *
- * <li>Changed: When the user selects to terminate by end time, the
- * final time step is adjusted to hit the final time exactly.
- * <br>
- * (Ryan Grove 2013/11/19)
- *
- * <li>Fixed: When using compressible models, we fixed up the right hand side
- * vector in a way so that the mean divergence is zero (even though it is of
- * course locally nonzero due to the compressibility). This is necessary to ensure
- * the solvability of the linear system, but it is wrong if the domain has open
- * boundaries through which fluid can escape or enter. We now only perform
- * this correction if there are no open boundaries and no boundaries with a
- * prescribed velocity.
- * <br>
- * (Wolfgang Bangerth 2013/11/19)
- *
- * <li>New: It is now possible to prescribe the velocity only for certain
- * components in the 'Prescribed velocity boundary indicators' parameter.
- * <br>
- * (Timo Heister 2013/11/08)
- *
- * <li>New: the "iterated Stokes" nonlinear solver will now stop iterating
- * if the residual is smaller than the new "Nonlinear solver tolerance".
- * <br>
- * (Timo Heister 2013/11/02)
- *
- * <li>New: add a visual postprocessor that outputs the artificial
- * viscosity parameter for the temperature equation on each cell.
- * <br>
- * (Timo Heister 2013/10/28)
- *
- * <li>Fixed: Moved particle generation to a class, changed particle
- * integration and generation to be factory patterned classes. There
- * should be no effect on the user but this will allow for easier
- * extension of particle functionality in the future.
- * <br>
- * (Eric Heien 2013/10/14)
- *
- * <li>New: Aspect now not only generates a <code>solution-NNNNN.visit</code>
- * file for each time step but also a global <code>solution.visit</code> file
- * that Visit can use to visualize the entire time dependent solution. (Both
- * of these work with versions of Visit that support this, including Visit 2.5.0.
- * Unfortunately, versions of Visit between 2.5.1 and the version current at
- * the time of writing this, 2.6.3, have a bug that prevents this.)
- * <br>
- * (Wolfgang Bangerth 2013/10/08)
- *
- * <li>Fixed: Performance of matrix assembly has been improved significantly,
- * especially in 3d: assembly of the temperature system is up to three
- * times faster, assembly of the Stokes system up to 50%.
- * <br>
- * (Timo Heister, Thomas Geenen, Wolfgang Bangerth 2013/10/08)
- *
- * <li>New: HDF5/XDMF will only output mesh data when the mesh changes,
- * reducing total data output significantly. XDMF serialization is also
- * properly implemented.
- * <br>
- * (Eric Heien, 2013/09/27)
- *
- * <li>New: HDF5 output now uses DataOutFilter to remove redundant
- * vertices/values in output data.
- * <br>
- * (Eric Heien, 2013/09/27)
- *
- * <li>New: Aspect now supports periodic domains (a recent development version of deal.II
- * is required).
- * <br>
- * (Ian Rose, Timo Heister, 2013/09/11)
- *
- * <li>New: The manual now has a new section discussing ways to make computations
- * go faster.
- * <br>
- * (Wolfgang Bangerth, 2013/09/03)
- *
- * <li>Fixed: The assembly of the temperature and compositional linear systems
- * in each time step used an unnecessarily large number of quadrature points.
- * This is now fixed.
- * <br>
- * (Thomas Geenen, 2013/08/30)
- *
- * <li>Extended: The ability to compute with tracers has been completely
- * overhauled. In particular, there is now a cookbook in the manual that
- * describes how to use them.
- * <br>
- * (Wolfgang Bangerth, 2013/08/13)
- *
- * <li>Added: ability to terminate simulation after
- * specified number of steps. This is implemented as one of the
- * terminator modules that can be selected from the input file.
- * <br>
- * (Ted Studley, 2013/07/03)
- *
- * <li>Added: new initial conditions for the Box geometry
- * to test different shaped inclusions.
- * <br>
- * (Ted Studley, 2013/06/20)
- *
- * <li>Removed: The parameter "Nonlinear iteration" was
- * not used anywhere so it got removed. You might need
- * to delete this line from your prm files.
- * <br>
- * (Timo Heister, 2013/06/20)
- *
- * <li>New: Nonlinear solver scheme = 'Stokes only' only
- * solves the Stokes system and ignores temperature and
- * compositional fields.
- * <br>
- * (Timo Heister, 2013/06/20)
- *
- * <li>New: If the underlying deal.II version supports this,
- * then VTK or VTU files now contain information about the time
- * and time step number corresponding to each file, and this
- * is then displayed when using Visit as the visualization
- * program.
- * <br>
- * (Wolfgang Bangerth, 2013/06/16)
- *
- * <li>New: In order to implement extensions, in particular
- * new plugins for material models, geometries, etc, it used to
- * be necessary to put the new files into the Aspect source
- * directories and re-compile all of Aspect. This is now no
- * longer necessary: You can just compile your additional
- * plugins into a shared library and tell Aspect via the
- * parameter file to load this shared library at start-up.
- * Details on this process are provided in the manual in
- * the section "How to write a plugin".
- * <br>
- * (Wolfgang Bangerth, 2013/06/16)
+ * <li>New: There is now a cookbook describing the usage of the GPlates plugin
+ * and possible applications. The internal velocity representation in the
+ * plugin was changed to cartesian and a smoothing algorithm was introduced.
+ * <br>
+ * (Rene Gassmoeller, Wolfgang Bangerth, 2014/04/12)
+ *
+ * <li>New: A global parameter ``Maximum time step'' allows the user to select
+ * the largest time step that a simulation can take. This may be useful for
+ * complicated models or benchmarking.
+ * <br>
+ * (Ian Rose, Wolfgang Bangerth, 2014/04/12)
+ *
+ * <li>Fixed: The simple material model now ignores negative compositional
+ * values that can occur from numerical undershots and even interpolation onto
+ * the FE space. This makes the cookbook/composition-active.prm work again.
+ * <br>
+ * (Timo Heister, 2014/04/08)
+ *
+ * <li>New: New options to remove rotational/translational modes from the
+ * solution.
+ * <br>
+ * (Ian Rose, Timo Heister, 2014/04/07)
+ *
+ * <li>New: A geometry model implementing a full sphere. There is also a
+ * corresponding gravity model where gravity increases linearly as you move
+ * outward.
+ * <br>
+ * (Ian Rose, 2014/04/07)
+ *
+ * <li>New: The box geometry allows you to specify a repetition argument in
+ * each coordinate direction.
+ * <br>
+ * (Timo Heister, 2014/04/07)
+ *
+ * <li>New: On startup, ASPECT now prints out whether it is running in debug
+ * or optimized mode. This is now part of a general status message at the top
+ * of every run.
+ * <br>
+ * (Wolfgang Bangerth, Juliane Dannberg, 2014/04/7)
+ *
+ * <li>Changed: The GPlates plugin for surface velocities always interpreted
+ * the start time of the model and the time increment between individual input
+ * files in seconds. It now honors the 'Use years in output instead of
+ * seconds' flag in the input file.
+ * <br>
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