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[ehsan benabbas <question688165@xxxxxxxxxxxxxxxxxxxxx>]

New question #688165 on Yade:
https://answers.launchpad.net/yade/+question/688165

Hi everyone,

I am using Ubuntu 18.04, and Yade 2019-08-08.git-775ae74

I use the Triaxial code by Bruno Chareyre [1] to run triaxial simulation on my specimen and only made the following changes in [1]:

num_spheres=20000,
targetPorosity = 0.4
young=200000000
poisson=1
mn,mx=Vector3(0,0,0),Vector3(0.02,0.02,0.02)
sigmaIso=-500000
particleDensity=2000
O.materials.append(FrictMat(young=young,poisson=poisson,frictionAngle=radians(compFricDegree),density=particleDensity,label='spheres'))
from yade import pack
sp=pack.SpherePack()
clumps=False
volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])
sp.makeCloud(mn,mx,0.0002,0.5,num_spheres,False, 0.95,seed=1)
O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
triax.goal1 = sigmaIso
triax.goal2 = sigmaIso
triax.goal3 = sigmaIso
f unb<stabilityThreshold and abs(sigmaIso-triax.meanStress)/sigmaIso<0.001:
triax.goal1 = sigmaIso
triax.goal2 = rate
triax.goal3 = sigmaIso

[1] https://gitlab.com/yade-dev/trunk/blob/master/examples/triax-tutorial/script-session1.py

***********************************************

The code can be run up to opening 3 windows (plot, show3D,remote) and I get the "END" message on the screen successfully. My problem is that when I press the "Play" button, nothing happens and then I get the following error:

============ RECORD AND PLOT DATA ============
/home/ehsan/yade/install/lib/x86_64-linux-gnu/yade-2019-08-08.git-775ae74/py/yade/plot.py:444: MatplotlibDeprecationWarning: 
The 'verts' kwarg was deprecated in Matplotlib 3.0 and will be removed in 3.2. Use 'marker' instead.
  scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw)
************** END **************
Analysis has been taken for 987.977 seconds or 16.466283333333333 minutes
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]]

Unhandled exception in thread started by <function liveUpdate at 0x7f3808480730>
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/yade/install/lib/x86_64-linux-gnu/yade-2019-08-08.git-775ae74/py/yade/plot.py in liveUpdate(timestamp)
    512                         for ax in axes:
    513                                 try:
--> 514                                         ax.relim() # recompute axes limits
    515                                         ax.autoscale_view()
    516                                 except RuntimeError: pass # happens if data are being updated and have not the same dimension at the very moment

~/.local/lib/python3.6/site-packages/matplotlib/axes/_base.py in relim(self, visible_only)
   2049         for line in self.lines:
   2050             if not visible_only or line.get_visible():
-> 2051                 self._update_line_limits(line)
   2052 
   2053         for p in self.patches:

~/.local/lib/python3.6/site-packages/matplotlib/axes/_base.py in _update_line_limits(self, line)
   1922         Figures out the data limit of the given line, updating self.dataLim.
   1923         """
-> 1924         path = line.get_path()
   1925         if path.vertices.size == 0:
   1926             return

~/.local/lib/python3.6/site-packages/matplotlib/lines.py in get_path(self)
   1025         """
   1026         if self._invalidy or self._invalidx:
-> 1027             self.recache()
   1028         return self._path
   1029 

~/.local/lib/python3.6/site-packages/matplotlib/lines.py in recache(self, always)
    677             y = self._y
    678 
--> 679         self._xy = np.column_stack(np.broadcast_arrays(x, y)).astype(float)
    680         self._x, self._y = self._xy.T  # views
    681 

<__array_function__ internals> in broadcast_arrays(*args, **kwargs)

~/.local/lib/python3.6/site-packages/numpy/lib/stride_tricks.py in broadcast_arrays(*args, **kwargs)
    262     args = [np.array(_m, copy=False, subok=subok) for _m in args]
    263 
--> 264     shape = _broadcast_shape(*args)
    265 
    266     if all(array.shape == shape for array in args):

~/.local/lib/python3.6/site-packages/numpy/lib/stride_tricks.py in _broadcast_shape(*args)
    189     # use the old-iterator because np.nditer does not handle size 0 arrays
    190     # consistently
--> 191     b = np.broadcast(*args[:32])
    192     # unfortunately, it cannot handle 32 or more arguments directly
    193     for pos in range(32, len(args), 31):

ValueError: shape mismatch: objects cannot be broadcast to a single shape
In [1]:   

Thank you for your help
Bests,
Ehsan

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