Adds an updated version of the Jupyter notebook tutorial for the onse…

…t of convection

cookbooks/convection-box/tutorial-onset-of-convection/README.md

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+Author: Lorraine J. Hwang, Ian Rose, Juliane Dannberg and the ASPECT development community
+
+# Introduction to ASPECT
+
+This notebook is based on tutorials by J. Dannberg that provide a basic introduction to ASPECT.
+This notebook demonstrates the onset of convection and the Nusselt-Rayleigh number relationship.
+
+To run, copy the contents of this directory to your workspace.
+
+
+## Running using ASPECT Jupyter Notebooks tool
+
+The current version is verified to run within the ASPECT Jupyter Notebooks tool which can be launched from the CIG website:
+
+https://geodynamics.org/resources/aspectnotebook
+
+
+## Running on your desktop
+
+If you run in your local JupyterLab environment, note the following dependencies:
+
+ * Python 3.8.5
+ * IPython 7.19.0
+ * Jupyterlab 3.2.1
+ * Jupyter widget extension 1.0.0 (see Appendix B)
+ * matplotlib 3.3.2
+ * numpy 1.19.2
+ * tables
+ * ipympl
+ * scipy
+ * glob
+
+
+## Running using Docker
+The current version of the docker container supports an older version of ASPECT.  The model_input directory contains two files with `_old` in its name which will work with this container.
+
+Use at your own risk.
+
+Here are the old instructions
+
+A. Install Docker
+
+B. Download the docker image
+> docker pull tjhei/aspect-jupyter
+
+1. Start Docker
+2. In a terminal window, navigate to directory where your model input is located:
+>	cd my_directory/ModelInput
+3. Load the Jupyter extension for widgets:
+>jupyter nbextension enable widgetsnbextension --py --sys-prefix
+4. Spin up Timo’s container with Jupyter notebooks and map your current working directory as input: 
+>	docker run -it -v "$(pwd):/home/dealii/aspect/model_input:ro" -d -p 8888:8888 --name tmpnb-aspect-jupyter tjhei/aspect-jupyter start-notebook.sh --NotebookApp.token=' ' 
+5. In a browser, type:
+>	http://localhost:8888/tree?
+6. Upload this notebook and the image files.
+
+Remember you are now running in a Docker container and NOT your desktop.
+
+**Common problems:**
+
+	unexpected error address already in use.
+	change your local host address 8887:8888
+	change this to 8887 in step 5
+
+You have to remove (or rename) that container to be able to reuse that name.
+Easiest solution (somewhat heavy handed) stop your container, prune, and check.
+
+> docker stop CONTAINER_ID
+
+> docker container prune 
+
+> docker ps -a
+ 
+## Packages install
+
+The heat flux slider requires the installation of two additional packages.
+
+**Adding Jupyter widgets**
+
+You should have added this in Step 3 above:
+> jupyter nbextension enable widgetsnbextension --py --sys-prefix
+
+**Installing tables**
+> conda install tables
+ 
+

cookbooks/convection-box/tutorial-onset-of-convection/model_input/.ipynb_checkpoints/convection-box2-old-checkpoint.prm

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+# 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
+
+# There are several global variables that have to do with what
+# time system we want to work in and what the end time is. We
+# also designate an output directory.
+set Use years in output instead of seconds = false
+set End time                               = 0.1
+set Output directory                       = output-convection-box2
+
+# Then there are variables that describe the tolerance of
+# the linear solver as well as how the pressure should
+# be normalized. Here, we choose a zero average pressure
+# at the surface of the domain (for the current geometry, the
+# surface is defined as the top boundary).
+set Linear solver tolerance                = 1e-7
+set Temperature solver tolerance           = 1e-10
+
+set Pressure normalization                 = surface
+set Surface pressure                       = 0
+
+
+# Then come a number of sections that deal with the setup
+# of the problem to solve. The first one deals with the
+# geometry of the domain within which we want to solve.
+# The sections that follow all have the same basic setup
+# where we select the name of a particular model (here,
+# the box geometry) and then, in a further subsection,
+# set the parameters that are specific to this particular
+# model.
+subsection Geometry model
+  set Model name = box
+
+  subsection Box
+    set X extent = 1
+    set Y extent = 1
+  end
+end
+
+
+# The next section deals with the initial conditions for the
+# temperature (there are no initial conditions for the
+# velocity variable since the velocity is assumed to always
+# be in a static equilibrium with the temperature field).
+# There are a number of models with the 'function' model
+# a generic one that allows us to enter the actual initial
+# conditions in the form of a formula that can contain
+# constants. We choose a linear temperature profile that
+# matches the boundary conditions defined below plus
+# a small perturbation:
+subsection Initial temperature model
+  set Model name = function
+
+  subsection Function
+    set Variable names      = x,z
+    set Function constants  = p=0.01, L=1, pi=3.1415926536, k=1
+    set Function expression = (1.0-z) - p*cos(k*pi*x/L)*sin(pi*z)
+  end
+end
+
+
+# Then follows a section that describes the boundary conditions
+# for the temperature. The model we choose is called 'box' and
+# allows to set a constant temperature on each of the four sides
+# of the box geometry. In our case, we choose something that is
+# heated from below and cooled from above. (As will be seen
+# in the next section, the actual temperature prescribed here
+# at the left and right does not matter.)
+subsection Boundary temperature model
+  set Model name = box
+
+  subsection Box
+    set Bottom temperature = 1
+    set Left temperature   = 0
+    set Right temperature  = 0
+    set Top temperature    = 0
+  end
+end
+
+
+# We then also have to prescribe several other parts of the model such as
+# which boundaries actually carry a prescribed boundary temperature, whereas
+# all other parts of the boundary are insulated (i.e., no heat flux through
+# these boundaries; this is also often used to specify symmetry boundaries).
+subsection Model settings
+  set Fixed temperature boundary indicators   = bottom, top
+
+  # The next parameters then describe on which parts of the
+  # boundary we prescribe a zero or nonzero velocity and
+  # on which parts the flow is allowed to be tangential.
+  # Here, all four sides of the box allow tangential
+  # unrestricted flow but with a zero normal component:
+  set Zero velocity boundary indicators       =
+  set Prescribed velocity boundary indicators =
+  set Tangential velocity boundary indicators = left, right, bottom, top
+end
+
+# The following two sections describe first the
+# direction (vertical) and magnitude of gravity and the
+# material model (i.e., density, viscosity, etc). We have
+# discussed the settings used here in the introduction to
+# this cookbook in the manual already.
+subsection Gravity model
+  set Model name = vertical
+
+  subsection Vertical
+    set Magnitude = 1e4   # = Ra / Thermal expansion coefficient
+  end
+end
+
+
+subsection Material model
+  set Model name = simple # default:
+
+  subsection Simple model
+    set Reference density             = 1
+    set Reference specific heat       = 1
+    set Reference temperature         = 0
+    set Thermal conductivity          = 1
+    set Thermal expansion coefficient = 1
+    set Viscosity                     = 1
+  end
+end
+
+
+# The settings above all pertain to the description of the
+# continuous partial differential equations we want to solve.
+# The following section deals with the discretization of
+# this problem, namely the kind of mesh we want to compute
+# on. We here use a globally refined mesh without
+# adaptive mesh refinement.
+subsection Mesh refinement
+  set Initial global refinement                = 5
+  set Initial adaptive refinement              = 0
+  set Time steps between mesh refinement       = 0
+end
+
+
+# The final part is to specify what ASPECT should do with the
+# solution once computed at the end of every time step. The
+# process of evaluating the solution is called `postprocessing'
+# and we choose to compute velocity and temperature statistics,
+# statistics about the heat flux through the boundaries of the
+# domain, and to generate graphical output files for later
+# visualization. These output files are created every time
+# a time step crosses time points separated by 0.01. Given
+# our start time (zero) and final time (0.5) this means that
+# we will obtain 50 output files.
+subsection Postprocess
+  set List of postprocessors = velocity statistics, temperature statistics, heat flux statistics, visualization, heat flux map
+
+  subsection Visualization
+    set Time between graphical output = 0.00
+    set Output format = hdf5
+  end
+end
+