yade-dev team mailing list archive

[Janek Kozicki <janek_listy@xxxxx>]

noreply@xxxxxxxxxxxxx said:     (by the date of Tue, 06 Jul 2010 11:33:20 -0000)

>   1. LIVE PLOTTING (thanks to Janek for the idea and the suggestion of mtTkinter). Report bugs.

OK, I double checked this. bzr2324 runs fine:

janek@atak:~/tmp/YY/bin/bin$ ./yade-trunk -j 3 ./triaxial-test.py
Welcome to Yade bzr2324
TCP python prompt on localhost:9000, auth cookie `ucasey'
TCP info provider on localhost:21000
Running script ./triaxial-test.py
/usr/lib/python2.6/dist-packages/pytz/__init__.py:32: UserWarning: Module pylab was already imported from /usr/lib/pymodules/python2.6/pylab.py, but /usr/lib/pymodules/python2.6 is being added to sys.path
  from pkg_resources import resource_stream
[[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]]
Yade [1]: import yade.plot; yade.plot.plot();
Yade [2]: import yade.plot; yade.plot.plot();
Yade [3]: import yade.plot; yade.plot.plot();
Yade [4]: zsh: quit       ./yade-trunk -j 3 ./triaxial-test.py



While bzr2326 does not:

janek@atak:~/tmp/YY/bin/bin$ ./yade-trunk -j 3 ./triaxial-test.py
Welcome to Yade bzr2326
TCP python prompt on localhost:9001, auth cookie `aucesy'
TCP info provider on localhost:21001
Running script ./triaxial-test.py
/usr/lib/python2.6/dist-packages/pytz/__init__.py:32: UserWarning: Module pylab was already imported from /usr/lib/pymodules/python2.6/pylab.py, but /usr/lib/pymodules/python2.6 is being added to sys.path
  from pkg_resources import resource_stream
[[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]]
Yade [1]: import yade.plot; yade.plot.plot();
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/home/janek/tmp/YY/bin/lib/yade-trunk/py/yade/__init__.pyc in <module>()
----> 1 
      2 
      3 
      4 
      5 

/home/janek/tmp/YY/bin/lib/yade-trunk/py/yade/plot.py in plot(noShow)
    200         to save the figure to file automatically.
    201         """
--> 202         createPlots()
    203         global currLineRefs
    204         if not noShow:

/home/janek/tmp/YY/bin/lib/yade-trunk/py/yade/plot.py in createPlots()
    145                 # create y1 lines

    146                 for d in plots_p_y1:
--> 147                         line,=pylab.plot(data[p],data[d[0]],d[1])
    148                         currLineRefs.append(LineRef(line,data[p],data[d[0]]))
    149                 # create the legend


/usr/lib/pymodules/python2.6/matplotlib/pyplot.pyc in plot(*args, **kwargs)
   2139         ax.hold(hold)
   2140     try:
-> 2141         ret = ax.plot(*args, **kwargs)
   2142         draw_if_interactive()
   2143     finally:

/usr/lib/pymodules/python2.6/matplotlib/axes.pyc in plot(self, *args, **kwargs)
   3430         lines = []
   3431 
-> 3432         for line in self._get_lines(*args, **kwargs):
   3433             self.add_line(line)
   3434             lines.append(line)

/usr/lib/pymodules/python2.6/matplotlib/axes.pyc in _grab_next_args(self, *args, **kwargs)
    309                 return
    310             if len(remaining) <= 3:
--> 311                 for seg in self._plot_args(remaining, kwargs):
    312                     yield seg
    313                 return

/usr/lib/pymodules/python2.6/matplotlib/axes.pyc in _plot_args(self, tup, kwargs)
    279                 kw[k] = v
    280 
--> 281         y = np.atleast_1d(tup[-1])
    282 
    283         if len(tup) == 2:

/usr/lib/python2.6/dist-packages/numpy/lib/shape_base.pyc in atleast_1d(*arys)
    292     res = []
    293     for ary in arys:
--> 294         res.append(array(ary,copy=False,subok=True,ndmin=1))
    295     if len(res) == 1:
    296         return res[0]

ValueError: setting an array element with a sequence.
Yade [2]: 
Do you really want to exit ([y]/n)? y
Yade: normal exit.


Also, this error does not occur in bzr2324 (this time the plot data
is empty - nothing to plot, so I am avoiding previous crash). This
happens when closing the plot windows. I suppose that it is introduced
by mtTkinter which tries to call something that doesn't exist
anymore:

Welcome to Yade bzr2326
TCP python prompt on localhost:9001, auth cookie `kecydu'
TCP info provider on localhost:21001
Running script ./triaxial-test.py
/usr/lib/python2.6/dist-packages/pytz/__init__.py:32: UserWarning: Module pylab was already imported from /usr/lib/pymodules/python2.6/pylab.py, but /usr/lib/pymodules/python2.6 is being added to sys.path
  from pkg_resources import resource_stream
[[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]]
Yade [1]: import yade.plot; yade.plot.plot();
Yade [2]: invalid command name "139800048206304callit"
    while executing
"139800048206304callit"
    ("after" script)

Do you really want to exit ([y]/n)? y
Yade: normal exit.


I am attaching the script. I was trying to reproduce bug in uniax.py,
but I could not. Strange, could be that I've done some mistake in ma
script. And without liveplot it was handled gracefully.

best regards
-- 
Janek Kozicki                               http://janek.kozicki.pl/  |

#!/usr/local/bin/yade-trunk
# -*- coding: utf-8 -*-
# -*- encoding=utf-8 -*-

# Script to perform a typical triaxial test
#-----------------------------------------------------
# simulation parameters
#-----------------------------------------------------
size=(0.1,0.1,0.1)
young=15000000
local_poisson=0.5
frictionAngle=30

number_of_spheres=2000
std_dev_radius=0.5
avg_radius=0.0025

max_compression=0.3

iso_compaction=50000
lateral_confinement=50000

#-----------------------------------------------------
# materials
#-----------------------------------------------------
O.materials.append(FrictMat(	young=young,
				poisson=local_poisson,
				frictionAngle=radians(0),  # is set to zero for generating sample with low porosity. triax will set it later to good value, search for frictionAngle
				density=2600,
				label='granular_material'))

O.materials.append(FrictMat(	young=young,
				poisson=local_poisson,
				frictionAngle=radians(0),
				density=2600,
				label='frictionless_material'))

#-----------------------------------------------------
# geometry
#-----------------------------------------------------
from yade import pack
sphere_cloud=pack.SpherePack()

# add the walls
walls=yade.utils.aabbWalls(	extrema=((0,0,0),size),
				thickness=.001,
				oversizeFactor=1.2,
				material='frictionless_material')
wallIds=O.bodies.append(walls)

# add the cloud of spheres
sphere_cloud.makeCloud(	minCorner=(0,0,0),
		maxCorner=size,
		rMean=avg_radius,
		rRelFuzz=std_dev_radius,
		num=number_of_spheres,
		periodic=False,
		porosity=-1)

O.bodies.append([utils.sphere(	center,
				rad,
				material='granular_material')
				for center,rad in sphere_cloud])

#-----------------------------------------------------
# list of engines
#-----------------------------------------------------
triax=TriaxialCompressionEngine(
	wall_left_id=wallIds[0],
	wall_right_id=wallIds[1],
	wall_bottom_id=wallIds[2],
	wall_top_id=wallIds[3],
	wall_back_id=wallIds[4],
	wall_front_id=wallIds[5],
	internalCompaction=0,
	autoCompressionActivation=1,
	sigmaIsoCompaction=iso_compaction,
	sigmaLateralConfinement=lateral_confinement,
	max_vel=1,
	StabilityCriterion=0.01,
	strainRate=0.1,
	frictionAngleDegree=frictionAngle,
	fixedPorosity=1, # ??
	epsilonMax=max_compression,
	thickness=0.001,
	autoUnload=1,
	autoStopSimulation=0,
	noFiles=0,
	maxMultiplier=1.01,
	finalMaxMultiplier=1.001,
	radiusControlInterval=10,
	stiffnessUpdateInterval=10,
	fixedPoroCompaction=0
)

O.engines=[
	ForceResetter(),
	BoundDispatcher([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()]),
	InsertionSortCollider(nBins=5,sweepLength=avg_radius*0.05),
	InteractionDispatchers(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_Basic()]
	),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=50),
	triax,
	NewtonIntegrator(damping=.3),
	PeriodicPythonRunner(iterPeriod=10,command='plot1()'),
]

#-----------------------------------------------------
# time step
#-----------------------------------------------------
#O.dt=-1.
O.dt=.5*utils.PWaveTimeStep() # initial timestep, to not explode right away

#-----------------------------------------------------
# plot some results
#-----------------------------------------------------
from yade import plot

def void_ratio():
	p=triax.porosity  # p=Vo/V
	V=triax.boxVolume
	Vo=p*V
	Vs=V-Vo
	#Vs=triax.spheresVolume
	#V=triax.boxVolume
	#Vo=V-Vs
	return Vo/Vs

plot.plots={'epsilon_1':('sigma_1',None,'porosity','void_ratio')}
#plot.labels={'sigma_1':'$\sigma_{1}$' , 'epsilon_1':'$\epsilon_{1}$' , 'void_ratio':'void ratio'}

def plot1():
	if(triax.currentState==3):  ## - make the plot only after compression has started
		plot.addData(
			sigma_1=triax.stress(1),
			epsilon_1=triax.strain[1],
			porosity=triax.porosity,
			void_ratio=void_ratio(),
		     )

#-----------------------------------------------------
# run!
#-----------------------------------------------------
from yade import qt
qt.View()
qt.Controller()
O.run(100,True)
O.dt=-1
O.run()
#O.wait()
#plot.plot()