.. _tutorialDataMining:

Data mining
=============

Read
-----

Local data
^^^^^^^^^^^

All data of the simulation are accessible from python; when you open the *Inspector*, blue labels of various data can be clicked -- left button for getting to the documentation, middle click to copy the name of the object (use ``Ctrl-V`` or middle-click to paste elsewhere). The interesting objects are among others (see :yref:`Omega` for a full list):

#. :yref:`O.engines<Omega.engines>`
   
   Engines are accessed by their index (position) in the simulation loop::

   	O.engines[0]      # first engine
   	O.engines[-1]     # last engine

   .. note:: The index can change if :yref:`O.engines<Omega.engines>` is modified. *Labeling* introduced in the section below is a better solution for reliable access to a particular engine.

#. :yref:`O.bodies<Omega.bodies>`

   Bodies are identified by their :yref:`id<Body.id>`, which is guaranteed to not change during the whole simulation::

   	O.bodies[0]                                                         # first body
   	[b.shape.radius for b in O.bodies if isinstance(b.shape,Sphere)]    # list of radii of all spherical bodies
   	sum([b.state.mass for b in O.bodies])                               # sum of masses of all bodies
   	numpy.average([b.state.vel[0] for b in O.bodies])                   # average velocity in x direction

   .. note:: Uniqueness of :yref:`Body.id` is not guaranteed, since newly created bodies might recycle :yref:`ids<Body.id>` of :yref:`deleted<BodyContainer.erase>` ones.

#. :yref:`O.forces<Omega.forces>`

   Generalized forces (forces, torques) acting on each particle. They are (usually) reset at the beginning of each step with :yref:`ForceResetter`, subsequently forces from individual interactions are accumulated in :yref:`InteractionLoop`. To access the data, use::

   	O.forces.f(0)     # force on #0
   	O.forces.t(1)     # torque on #1
	
#. :yref:`O.interactions<Omega.interactions>`

   Interactions are identified by :yref:`ids<Body.id>` of the respective interacting particles (they are created and deleted automatically during the simulation)::

   	O.interactions[0,1]   # interactions of #0 with #1
   	O.interactions[1,0]   # the same object
   	O.bodies[0].intrs()   # all interactions of body #0
   	for i in O.bodies[12].intrs(): print (i.isReal,i.id1,i.id2)    # get some info about interactions of body #12
   	[(i.isReal,i.id1,i.id2) for i in O.bodies[12].intrs()]         # same thing, but make a list

Labels
"""""""

:yref:`Engines<Engine>` and :yref:`functors<Functor>` can be *labeled*, which means that python variable of that name is automatically created.

.. ipython::

	@suppress
	Yade [1]: from yade import *
	
	Yade [1]: O.engines=[
	   ...:    NewtonIntegrator(damping=.2,label='newtonCustomLabel')
	   ...: ]
	   ...:

	Yade [1]: newtonCustomLabel.damping=.4

	Yade [1]: O.engines[0].damping              # O.engines[0] and newtonCustomLabel are the same objects

        Yade [1]: newtonCustomLabel==O.engines[0]   # O.engines[0] and newtonCustomLabel are the same objects

.. rubric:: Exercises

#. Find meaning of this
   expression::

   	max([b.state.vel.norm() for b in O.bodies])

#. Run the :ref:`gravity-deposition` script, pause after a few seconds of simulation. Write expressions that compute

   #. kinetic energy $\sum \frac{1}{2} m_i |v_i| ^2$
   #. average mass (hint: use `numpy.average <http://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html>`__)
   #. maximum $z$-coordinate of all particles
   #. number of interactions of body #1

Global data
^^^^^^^^^^^

Useful measures of what happens in the simulation globally:

unbalanced force
	ratio of maximum contact force and maximum per-body force; measure of staticity, computed with :yref:`unbalancedForce<yade._utils.unbalancedForce>`.
porosity
	ratio of void volume and total volume; computed with :yref:`porosity<yade._utils.porosity>`.
coordination number
	average number of interactions per particle, :yref:`avgNumInteractions<yade.utils.avgNumInteractions>`
stress tensor (periodic boundary conditions)
	averaged force in interactions, computed with :yref:`normalShearStressTensors<yade._utils.normalShearStressTensors>`
fabric tensor
	distribution of contacts in space (not yet implemented); can be visualized with :yref:`plotDirections<yade.utils.plotDirections>`

Energies
""""""""

Evaluating energy data for all components in the simulation (such as gravity work, kinetic energy, plastic dissipation, damping dissipation) can be enabled with ::

	O.trackEnergy=True

Subsequently, energy values are accessible in the :yref:`O.energy<Omega.energy>`; it is a dictionary where its entries can be retrived with ``keys()`` and their values with ``O.energy[key]``.

Save
----

PyRunner
^^^^^^^^^

To save data that we just learned to access, we need to call Python from within the *simulation loop*. :yref:`PyRunner` is created just for that; it inherits periodicy control from :yref:`PeriodicEngine` and takes the code to run as text (must be quoted, i.e. inside ``'...'``) attribute called *command*. For instance, adding this to :yref:`O.engines<Omega.engines>` will print the current step number every one second wall clock time::

	O.engines=O.engines+[ PyRunner(command='print(O.iter)',realPeriod=1) ]

Writing complicated code inside *command* is awkward; in such case, we define a function that will be called::

	def myFunction():
		'''Print step number, and pause the simulation is unbalanced force is smaller than 0.05.'''
		print(O.iter)
		if utils.unbalancedForce()<0.05:
			print('Unbalanced force is smaller than 0.05, pausing.')
			O.pause()

Now this function can be added to :yref:`O.engines<Omega.engines>`::

	O.engines+=[PyRunner(command='myFunction()',iterPeriod=100)]

or, in general, like that::

	O.engines=[
		# ...
		PyRunner(command='myFunction()',iterPeriod=100) # call myFunction every 100 steps
	]


.. comment: sphinx syntax examples: https://sphinx-rtd-theme.readthedocs.io/en/latest/demo/demo.html https://raw.githubusercontent.com/rtfd/sphinx_rtd_theme/master/docs/demo/demo.rst
..          https://github.com/sphinx-doc/sphinx/issues/2640

.. warning::
	If a function was declared inside a *live* yade session (`ipython <http://ipython.org>`_) and PyRunner attribute :yref:`updateGlobals is set to False <PyRunner.updateGlobals>` then an error ``NameError: name 'myFunction' is not defined`` will occur unless python globals() are updated with command

	.. code-block:: python

		globals().update(locals())


.. rubric:: Exercises

#. Run the :ref:`gravity-deposition` simulation, but change it such that:

   #. :yref:`yade._utils.unbalancedForce` is printed every 2 seconds.
   #. check every 1000 steps the value of unbalanced force

      * if smaller than 0.2, set :yref:`damping<NewtonIntegrator.damping>` to 0.8 (hint: use labels)
      * if smaller than 0.1, pause the simulation

Keeping history
^^^^^^^^^^^^^^^^^

Yade provides the :yref:`yade.plot` module used for storing and plotting variables (plotting itself will be discussed later). Let us start by importing this module and declare variable names that will be plotted::

	from yade import plot
	plot.plots={'t':('coordNum','unForce',None,'Ek')}                # kinetic energy will have legend on the right as indicated by None separator.

Periodic storing of data is done with :yref:`PyRunner` and the :yref:`yade.plot.addData` function. Also let's enable energy tracking::

	O.trackEnergy=True
	def addPlotData():
		# this function adds current values to the history of data, under the names specified
		plot.addData(t=O.time,Ek=utils.kineticEnergy(),coordNum=utils.avgNumInteractions(),unForce=utils.unbalancedForce())

Now this function can be added to :yref:`O.engines<Omega.engines>`::

	O.engines+=[PyRunner(command='addPlotData()',iterPeriod=20)]

or, in general, like that::

	O.engines=[  # ...,
		PyRunner(command='addPlotData()',iterPeriod=20)         # call the addPlotData function every 20 iterations
	]

History is stored in :yref:`yade.plot.data`, and can be accessed using the variable name, e.g. ``plot.data['Ek']``, and saved to text file (for post-processing outside yade) with :yref:`yade.plot.saveDataTxt`.

Plot
-----

:yref:`yade.plot` provides facilities for plotting history saved with :yref:`yade.plot.addData` as 2d plots. Data to be plotted are specified using dictionary :yref:`yade.plot.plots` ::

	plot.plots={'t':('coordNum','unForce',None,'Ek')}

History of all values is given as the name used for :yref:`yade.plot.addData`; keys of the dictionary are $x$-axis values, and values are sequence of data on the $y$ axis; the ``None`` separates data on the left and right axes (they are scaled independently). The plot itself is created with ::

	plot.plot()         # on the command line, F8 can be used as shorthand

While the plot is open, it will be updated periodically, so that simulation evolution can be seen in real-time.

Energy plots
^^^^^^^^^^^^^

Plotting all energy contributions would be difficult, since names of all energies might not be known in advance. Fortunately, there is a way to handle that in Yade. It consists in two parts:

#. :yref:`yade.plot.addData` is given all the energies that are currently defined::

  		plot.addData(i=O.iter,total=O.energy.total(),**O.energy)

   The :yref:`O.energy.total<EnergyTracker.total>` functions, which sums all energies together. The ``**O.energy`` is special python syntax for converting dictionary (remember that :yref:`O.energy<EnergyTracker>` is a dictionary) to named functions arguments, so that the following two commands are identical::

     function(a=3,b=34)              # give arguments as arguments
     function(**{'a':3,'b':34})      # create arguments from dictionary

#. Data to plot are specified using a *function* that gives names of data to plot, rather than providing the data names directly::

   	plot.plots={'i':['total']+O.energy.keys()}

   where ``total`` is the name we gave to ``O.energy.total()`` above, while ``O.energy.keys()`` will always return list of currently defined energies.

Energy plot example
"""""""""""""""""""

Plotting energies inside a *live* yade session, for example by launching :ysrc:`examples/test/triax-basic-without-plots.py` would look following::

	from yade import plot
	O.trackEnergy=True
	O.step()                          # performing a single simulation step is necessary to populate O.energy.keys()
	plot.plots={'t':O.energy.keys()+['total']}

	def addPlotData():
		# this function adds current values to the history of data, under the names specified
		plot.addData( t=O.time , total=O.energy.total() , **O.energy )

	O.engines+=[PyRunner(command='addPlotData()',iterPeriod=20)]

	globals().update(locals())        # do this only because this is an example of a live yade session

Press F8 to show plot window and F11 to show 3D view, then press ▶ to start simulation.

Using multiple plots
""""""""""""""""""""

It is also possible to make several separate plots, for example like this::

	plot.plots={ 't':('total','kinetic') , 't ':['elastPotential','gravWork'] , 't  ':('nonviscDamp') }

.. warning::
	There cannot be duplicate names declared in separate plots. This is why spaces were used above to indicate the same variable ``t``.

With the caveat above, a following example inside a *live* yade session launched on :ysrc:`examples/test/triax-basic-without-plots.py` would look following::

	from yade import plot
	O.trackEnergy=True
	plot.plots={ 't':('total','kinetic') , 't ':['elastPotential','gravWork'] , 't  ':('nonviscDamp') }

	def addPlotData():
		# assign value to all three: 't', 't ' and 't  ' with single t=... assignment
		plot.addData( t=O.time , total=O.energy.total() , **O.energy )

	O.engines+=[PyRunner(command='addPlotData()',iterPeriod=20)]

	globals().update(locals())        # do this only because this is an example of a live yade session

	plot.plot(subPlots=False)         # show plots in separate windows

	plot.plot(subPlots=True)          # same as pressing F8: close current plot windows and reopen a single new one

Press F8 to show plot window and F11 to show 3D view, then press ▶ to start simulation, see `video`__ below:

__ https://youtu.be/AALiZ7G7yNM

.. youtube:: AALiZ7G7yNM


.. rubric:: Exercises

#. Calculate average momentum in y direction.
#. Run the :ref:`gravity-deposition` script, plotting unbalanced force and kinetic energy.
#. While the script is running, try changing the :yref:`NewtonIntegrator.damping` parameter (do it from both *Inspector* and from the command-line). What influence does it have on the evolution of unbalanced force and kinetic energy?
#. Think about and write down all energy sources (input); write down also all energy sinks (dissipation).
#. Simulate :ref:`gravity-deposition` and plot all energies as they evolve during the simulation.

.. seealso::
	
	Most :ref:`examples` use plotting facilities of Yade, some of them also track energy of the simulation.
