Yade

make doc error

Asked by hjz

Hi Yaders,
      After executing the order 'make install', installing yade by source code, I would like to build the documentation. But when I execute 'make doc', the errors come out. I would like to know how to solve it. And if it couldn't be solved, these errors have influence in using Yade?

      This is the output in the terminal:

hjz@hjz-ubuntu:~/yade2017/build$ sudo make doc
Scanning dependencies of target doc
Welcome to Yade 2017.01a
TCP python prompt on localhost:9000, auth cookie `dakuse'
XMLRPC info provider on http://localhost:21000
Running script yadeSphinx.py
warning: unable to convert `\araa'
warning: unable to convert `\aj'
warning: reference `dec' undefined
warning: unable to convert `\aap'
warning: reference `aug' undefined
Running Sphinx v1.3.6
WARNING: the config value 'my_maketitle' is set to a string with non-ASCII characters; this can lead to Unicode errors occurring. Please use Unicode strings, e.g. u'Content'.
WARNING: extension 'youtube' has no setup() function; is it really a Sphinx extension module?
building [mo]: all of 0 po files
building [html]: all source files
updating environment: 39 added, 0 changed, 0 removed
reading sources... [ 33%] introduction

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 117
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()

NameError: name 'yade' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 321
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies[100]

IndexError: Body id out of range.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 327
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies.append(s)

IndexError: Body already has id 0 set; appending such body (for the second time) is not allowed.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 382
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.interactions[100,10111]

IndexError: No such interaction
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 399
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.forces.addF(0,Vector3(1,2,3))

NameError: name 'Vector3' is not defined
<<<-------------------------------------------------------------------------

reading sources... [ 38%] prog

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 405
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 Vector3(1,2,3).cross(Vector3(0,0,1))

NameError: name 'Vector3' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 405
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 Quaternion(Vector3(0,0,1),pi/2)

NameError: name 'Quaternion' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 434
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 Sphere().name ## getClassName()

AttributeError: 'Sphere' object has no attribute 'name'
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 562
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.engines=[GravityEngine(gravity=Vector3(0,0,-9.81))]

NameError: name 'Vector3' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1466
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.forces.addF(0,Vector3(1,2,3))

NameError: name 'Vector3' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1466
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.forces.f(100)

IndexError: Body id out of range.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1636
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 f1.force=Vector3(0,-1,-2)

NameError: name 'Vector3' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1646
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 f2=ForceEngine(ids=[0,4,5],force=Vector3(0,-1,-2))

NameError: name 'Vector3' is not defined
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1646
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 print f2.dict()

NameError: name 'f2' is not defined
<<<-------------------------------------------------------------------------

reading sources... [ 58%] tutorial-hands-on

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 197
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 a[3] # error

IndexError: list index out of range
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 226
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 b[0]=4 # error

TypeError: 'tuple' object does not support item assignment
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 383
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies[1].shape.radius # radius of body #1 (will give error if not sphere, since only spheres have radius defined)

AttributeError: 'NoneType' object has no attribute 'shape'
<<<-------------------------------------------------------------------------

ERROR /home/hjz/yade2017/trunk/pkg/common/InsertionSortCollider.cpp:240 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.
reading sources... [ 64%] user

>>>-------------------------------------------------------------------------
Warning in /home/hjz/yade2017/build/doc/sphinx/user.rst at block ending on line 887
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:60: UserWarning: Overwriting yade.params.ab which already exists.
  if mark in yade.params.__dict__: warnings.warn('Overwriting yade.params.%s which already exists.'%mark)
<<<-------------------------------------------------------------------------
reading sources... [100%] yade.ymport
/home/hjz/yade2017/build/doc/sphinx/index-toctree-manuals.rst:6: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/index-toctree-reference.rst:5: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/index-toctree-theory.rst:5: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/publications.rst:127: WARNING: Inline emphasis start-string without end-string.
/home/hjz/yade2017/build/doc/sphinx/publications.rst:429: WARNING: Duplicate explicit target name: "maurin2015".
/home/hjz/yade2017/build/doc/sphinx/publications.rst:429: WARNING: duplicate citation Maurin2015, other instance in /home/hjz/yade2017/build/doc/sphinx/publications.rst
/home/hjz/yade2017/build/doc/sphinx/yade.wrapper.rst:1: WARNING: malformed hyperlink target.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/hjz/yade2017/build/doc/sphinx/consulting.rst:: WARNING: document isn't included in any toctree
/home/hjz/yade2017/build/doc/sphinx/index-toctree-book.rst:: WARNING: document isn't included in any toctree
/home/hjz/yade2017/build/doc/sphinx/index-toctree_manuals.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the pngmath_latex setting
writing output... [100%] yade.ymport
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:docstring of yade.utils.UnstructuredGrid:None: WARNING: more than one target found for cross-reference u'dict': yade.wrapper.Facet.dict, yade.wrapper.InsertionSortCollider.dict, yade.wrapper.ViscElCapMat.dict, yade.wrapper.LinearDragEngine.dict, yade.wrapper.Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.dict, yade.wrapper.CapillaryStressRecorder.dict, yade.wrapper.PFacet.dict, yade.wrapper.LawDispatcher.dict, yade.wrapper.FlowEngine_PeriodicInfo.dict, yade.wrapper.GridCoGridCoGeom.dict, yade.wrapper.CohesiveTriaxialTest.dict, yade.wrapper.NewtonIntegrator.dict, yade.wrapper.ViscElMat.dict, yade.wrapper.HydrodynamicsLawLBM.dict, yade.wrapper.CohFrictPhys.dict, yade.wrapper.Bo1_Polyhedra_Aabb.dict, yade.wrapper.Law2_ScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.IPhys.dict, yade.wrapper.GlobalStiffnessTimeStepper.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom6D.dict, yade.wrapper.Ip2_FrictMat_CpmMat_FrictPhys.dict, yade.wrapper.TetraVolumetricLaw.dict, yade.wrapper.KinemCNSEngine.dict, yade.wrapper.Gl1_GridConnection.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_HertzWithLinearShear.dict, yade.wrapper.GridNodeGeom6D.dict, yade.wrapper.CohesiveDeformableElementMaterial.dict, yade.wrapper.KinemSimpleShearBox.dict, yade.wrapper.Law2_L6Geom_FrictPhys_Linear.dict, yade.wrapper.L6Geom.dict, yade.wrapper.GlIPhysDispatcher.dict, yade.wrapper.CohFrictMat.dict, yade.wrapper.Bo1_PFacet_Aabb.dict, yade.wrapper.SumIntrForcesCb.dict, yade.wrapper.MindlinPhys.dict, yade.wrapper.Ip2_2xInelastCohFrictMat_InelastCohFrictPhys.dict, yade.wrapper.CpmStateUpdater.dict, yade.wrapper.Tetra.dict, yade.wrapper.Gl1_PolyhedraPhys.dict, yade.wrapper.HelixEngine.dict, yade.wrapper.ThreeDTriaxialEngine.dict, yade.wrapper.JCFpmState.dict, yade.wrapper.Bo1_Tetra_Aabb.dict, yade.wrapper.Law2_ScGeom_MortarPhys_Lourenco.dict, yade.wrapper.Ig2_Sphere_Sphere_L3Geom.dict, yade.wrapper.Box.dict, yade.wrapper.PolyhedraSplitter.dict, yade.wrapper.LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.TimeStepper.dict, yade.wrapper.Gl1_Box.dict, yade.wrapper.Gl1_Tetra.dict, yade.wrapper.TriaxialTest.dict, yade.wrapper.PeriTriaxController.dict, yade.wrapper.InternalForceFunctor.dict, yade.wrapper.AxialGravityEngine.dict, yade.wrapper.Gl1_PolyhedraGeom.dict, yade.wrapper.VTKRecorder.dict, yade.wrapper.Bo1_ChainedCylinder_Aabb.dict, yade.wrapper.Ip2_2xNormalInelasticMat_NormalInelasticityPhys.dict, yade.wrapper.Bound.dict, yade.wrapper.BubbleMat.dict, yade.wrapper.KinematicEngine.dict, yade.wrapper.RotationEngine.dict, yade.wrapper.ResetRandomPosition.dict, yade.wrapper.Ip2_CpmMat_CpmMat_CpmPhys.dict, yade.wrapper.FrictPhys.dict, yade.wrapper.Law2_ScGeom_BubblePhys_Bubble.dict, yade.wrapper.FieldApplier.dict, yade.wrapper.Gl1_CpmPhys.dict, yade.wrapper.PeriodicEngine.dict, yade.wrapper.NormPhys.dict, yade.wrapper.GenericSpheresContact.dict, yade.wrapper.BicyclePedalEngine.dict, yade.wrapper.TTetraSimpleGeom.dict, yade.wrapper.Body.dict, yade.wrapper.WirePhys.dict, yade.wrapper.Gl1_PFacet.dict, yade.wrapper.Interaction.dict, yade.wrapper.DeformableCohesiveElement.dict, yade.wrapper.TTetraGeom.dict, yade.wrapper.CohesiveFrictionalContactLaw.dict, yade.wrapper.Law2_CylScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.Collider.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_ScGeom.dict, yade.wrapper.Node.dict, yade.wrapper.PeriIsoCompressor.dict, yade.wrapper.LBMnode.dict, yade.wrapper.FrictViscoMat.dict, yade.wrapper.MicroMacroAnalyser.dict, yade.wrapper.Material.dict, yade.wrapper.GlBoundDispatcher.dict, yade.wrapper.Law2_ScGeom_ViscoFrictPhys_CundallStrack.dict, yade.wrapper.GridConnection.dict, yade.wrapper.GlExtra_OctreeCubes.dict, yade.wrapper.Gl1_Cylinder.dict, yade.wrapper.Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys.dict, yade.wrapper.Law2_ScGeom_FrictViscoPhys_CundallStrackVisco.dict, yade.wrapper.GlStateDispatcher.dict, yade.wrapper.Shape.dict, yade.wrapper.OpenGLRenderer.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormShearPhys.dict, yade.wrapper.ChCylGeom6D.dict, yade.wrapper.PolyhedraGeom.dict, yade.wrapper.Ig2_Facet_Polyhedra_PolyhedraGeom.dict, yade.wrapper.NormalInelasticityPhys.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraSimpleGeom.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom.dict, yade.wrapper.CapillaryPhys.dict, yade.wrapper.LawTester.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom.dict, yade.wrapper.ViscoFrictPhys.dict, yade.wrapper.GlobalEngine.dict, yade.wrapper.Gl1_NormPhys.dict, yade.wrapper.Clump.dict, yade.wrapper.IPhysFunctor.dict, yade.wrapper.Cylinder.dict, yade.wrapper.Ig2_GridNode_GridNode_GridNodeGeom6D.dict, yade.wrapper.SnapshotEngine.dict, yade.wrapper.TorqueRecorder.dict, yade.wrapper.ParallelEngine.dict, yade.wrapper.InelastCohFrictPhys.dict, yade.wrapper.Bo1_Box_Aabb.dict, yade.wrapper.FlowEngineT.dict, yade.wrapper.Ip2_ViscElMat_ViscElMat_ViscElPhys.dict, yade.wrapper.PersistentTriangulationCollider.dict, yade.wrapper.Bo1_Wall_Aabb.dict, yade.wrapper.Ig2_Wall_Sphere_L3Geom.dict, yade.wrapper.TriaxialStateRecorder.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom.dict, yade.wrapper.Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.MortarMat.dict, yade.wrapper.Ig2_Wall_PFacet_ScGeom.dict, yade.wrapper.LudingMat.dict, yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement.dict, yade.wrapper.Gl1_Node.dict, yade.wrapper.Ip2_FrictMat_FrictMat_ViscoFrictPhys.dict, yade.wrapper.ZECollider.dict, yade.wrapper.Ip2_MortarMat_MortarMat_MortarPhys.dict, yade.wrapper.IntrCallback.dict, yade.wrapper.TesselationWrapper.dict, yade.wrapper.StepDisplacer.dict, yade.wrapper.ElasticContactLaw.dict, yade.wrapper.GlShapeDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys.dict, yade.wrapper.Lin4NodeTetra.dict, yade.wrapper.IGeom.dict, yade.wrapper.Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D.dict, yade.wrapper.Dispatcher.dict, yade.wrapper.CombinedKinematicEngine.dict, yade.wrapper.LBMlink.dict, yade.wrapper.Law2_ScGeom_LudingPhys_Basic.dict, yade.wrapper.Ip2_WireMat_WireMat_WirePhys.dict, yade.wrapper.Law2_ScGeom_ViscElCapPhys_Basic.dict, yade.wrapper.SimpleShear.dict, yade.wrapper.Bo1_Sphere_Aabb.dict, yade.wrapper.Engine.dict, yade.wrapper.ScGeom6D.dict, yade.wrapper.LudingPhys.dict, yade.wrapper.LBMbody.dict, yade.wrapper.KinemCNLEngine.dict, yade.wrapper.KinemCNDEngine.dict, yade.wrapper.WireState.dict, yade.wrapper.DragEngine.dict, yade.wrapper.CircularFactory.dict, yade.wrapper.Gl1_Sphere.dict, yade.wrapper.Scene.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormPhys.dict, yade.wrapper.Gl1_Aabb.dict, yade.wrapper.GlShapeFunctor.dict, yade.wrapper.Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys.dict, yade.wrapper.TriaxialStressController.dict, yade.wrapper.ChainedState.dict, yade.wrapper.Law2_GridCoGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HarmonicMotionEngine.dict, yade.wrapper.Law2_ScGridCoGeom_CohFrictPhys_CundallStrack.dict, yade.wrapper.RadialForceEngine.dict, yade.wrapper.Functor.dict, yade.wrapper.GeneralIntegratorInsertionSortCollider.dict, yade.wrapper.ScGridCoGeom.dict, yade.wrapper.IGeomDispatcher.dict, yade.wrapper.ElastMat.dict, yade.wrapper.Law2_ScGeom_ViscElPhys_Basic.dict, yade.wrapper.MatchMaker.dict, yade.wrapper.ServoPIDController.dict, yade.wrapper.GlIGeomFunctor.dict, yade.wrapper.Law2_CylScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HdapsGravityEngine.dict, yade.wrapper.CylScGeom6D.dict, yade.wrapper.Ig2_Sphere_GridConnection_ScGridCoGeom.dict, yade.wrapper.Cell.dict, yade.wrapper.JCFpmPhys.dict, yade.wrapper.WireMat.dict, yade.wrapper.Serializable.dict, yade.wrapper.NormShearPhys.dict, yade.wrapper.SpheresFactory.dict, yade.wrapper.Law2_ScGeom_CpmPhys_Cpm.dict, yade.wrapper.Bo1_Facet_Aabb.dict, yade.wrapper.GravityEngine.dict, yade.wrapper.Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.KinemCTDEngine.dict, yade.wrapper.BubblePhys.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinPhys.dict, yade.wrapper.BoundDispatcher.dict, yade.wrapper.InterpolatingHelixEngine.dict, yade.wrapper.Law2_ScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.Bo1_GridConnection_Aabb.dict, yade.wrapper.Ip2_BubbleMat_BubbleMat_BubblePhys.dict, yade.wrapper.BoundFunctor.dict, yade.wrapper.Bo1_Cylinder_Aabb.dict, yade.wrapper.Law2_TTetraSimpleGeom_NormPhys_Simple.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom.dict, yade.wrapper.Integrator.dict, yade.wrapper.MindlinCapillaryPhys.dict, yade.wrapper.Gl1_Polyhedra.dict, yade.wrapper.IPhysDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictMat_FrictPhys.dict, yade.wrapper.If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.NormalInelasticMat.dict, yade.wrapper.FacetTopologyAnalyzer.dict, yade.wrapper.GlIPhysFunctor.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.dict, yade.wrapper.SpatialQuickSortCollider.dict, yade.wrapper.Gl1_L3Geom.dict, yade.wrapper.PeriodicFlowEngine.dict, yade.wrapper.Law2_L3Geom_FrictPhys_ElPerfPl.dict, yade.wrapper.TriaxialCompressionEngine.dict, yade.wrapper.Disp2DPropLoadEngine.dict, yade.wrapper.JCFpmMat.dict, yade.wrapper.PolyhedraMat.dict, yade.wrapper.RungeKuttaCashKarp54Integrator.dict, yade.wrapper.GlStateFunctor.dict, yade.wrapper.Bo1_DeformableElement_Aabb.dict, yade.wrapper.BoundaryController.dict, yade.wrapper.TranslationEngine.dict, yade.wrapper.InelastCohFrictMat.dict, yade.wrapper.Law2_ScGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.DeformableElementMaterial.dict, yade.wrapper.GlIGeomDispatcher.dict, yade.wrapper.TorqueEngine.dict, yade.wrapper.FrictViscoPhys.dict, yade.wrapper.Recorder.dict, yade.wrapper.ChainedCylinder.dict, yade.wrapper.Polyhedra.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraGeom.dict, yade.wrapper.FEInternalForceEngine.dict, yade.wrapper.Ip2_FrictMat_PolyhedraMat_FrictPhys.dict, yade.wrapper.Gl1_Wall.dict, yade.wrapper.CpmMat.dict, yade.wrapper.LawFunctor.dict, yade.wrapper.CpmState.dict, yade.wrapper.Sphere.dict, yade.wrapper.LinCohesiveElasticMaterial.dict, yade.wrapper.Gl1_L6Geom.dict, yade.wrapper.LinIsoRayleighDampElastMat.dict, yade.wrapper.BoxFactory.dict, yade.wrapper.Law2_ScGeom_CapillaryPhys_Capillarity.dict, yade.wrapper.Ig2_Wall_Polyhedra_PolyhedraGeom.dict, yade.wrapper.FlowEngine.dict, yade.wrapper.Wall.dict, yade.wrapper.PolyhedraPhys.dict, yade.wrapper.Gl1_DeformableElement.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom6D.dict, yade.wrapper.InteractionLoop.dict, yade.wrapper.Ig2_Sphere_PFacet_ScGridCoGeom.dict, yade.wrapper.CapillaryTriaxialTest.dict, yade.wrapper.MortarPhys.dict, yade.wrapper.Gl1_Facet.dict, yade.wrapper.PyRunner.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom6D.dict, yade.wrapper.CentralGravityEngine.dict, yade.wrapper.UniaxialStrainer.dict, yade.wrapper.FrictMat.dict, yade.wrapper.CylScGeom.dict, yade.wrapper.GlExtra_LawTester.dict, yade.wrapper.Law2_ScGeom_WirePhys_WirePM.dict, yade.wrapper.InternalForceDispatcher.dict, yade.wrapper.Ig2_Sphere_Sphere_L6Geom.dict, yade.wrapper.Law2_PolyhedraGeom_PolyhedraPhys_Volumetric.dict, yade.wrapper.GridNode.dict, yade.wrapper.FileGenerator.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom6D.dict, yade.wrapper.Ig2_PFacet_PFacet_ScGeom.dict, yade.wrapper.CpmPhys.dict, yade.wrapper.Ig2_Facet_Sphere_L3Geom.dict, yade.wrapper.ForceResetter.dict, yade.wrapper.Ip2_FrictMat_FrictMat_CapillaryPhys.dict, yade.wrapper.ViscElPhys.dict, yade.wrapper.EnergyTracker.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom.dict, yade.wrapper.Ig2_GridConnection_GridConnection_GridCoGridCoGeom.dict, yade.wrapper.Aabb.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_MindlinDeresiewitz.dict, yade.wrapper.GlBoundFunctor.dict, yade.wrapper.State.dict, yade.wrapper.ScGeom.dict, yade.wrapper.Peri3dController.dict, yade.wrapper.InterpolatingDirectedForceEngine.dict, yade.wrapper.ForceRecorder.dict, yade.wrapper.Ig2_GridConnection_PFacet_ScGeom.dict, yade.wrapper.PartialEngine.dict, yade.wrapper.ViscElCapPhys.dict, yade.wrapper.L3Geom.dict, yade.wrapper.FlatGridCollider.dict, yade.wrapper.DeformableElement.dict, yade.wrapper.Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.dict, yade.wrapper.Ip2_LudingMat_LudingMat_LudingPhys.dict, yade.wrapper.LinIsoElastMat.dict, yade.wrapper.HarmonicRotationEngine.dict, yade.wrapper.Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity.dict, yade.wrapper.ForceEngine.dict, yade.wrapper.Bo1_Node_Aabb.dict, yade.wrapper.Ig2_Sphere_Polyhedra_ScGeom.dict, yade.wrapper.IGeomFunctor.dict, yade.wrapper.Ig2_Wall_Sphere_ScGeom.dict, yade.wrapper.DomainLimiter.dict, yade.wrapper.Gl1_ChainedCylinder.dict, yade.wrapper.If2_Lin4NodeTetra_LinIsoRayleighDampElast.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeom.dict, yade.wrapper.GlExtraDrawer.dict, yade.wrapper.HydroForceEngine.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_Mindlin.dict
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:docstring of yade.utils.UnstructuredGrid:None: WARNING: more than one target found for cross-reference u'dict': yade.wrapper.Facet.dict, yade.wrapper.InsertionSortCollider.dict, yade.wrapper.ViscElCapMat.dict, yade.wrapper.LinearDragEngine.dict, yade.wrapper.Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.dict, yade.wrapper.CapillaryStressRecorder.dict, yade.wrapper.PFacet.dict, yade.wrapper.LawDispatcher.dict, yade.wrapper.FlowEngine_PeriodicInfo.dict, yade.wrapper.GridCoGridCoGeom.dict, yade.wrapper.CohesiveTriaxialTest.dict, yade.wrapper.NewtonIntegrator.dict, yade.wrapper.ViscElMat.dict, yade.wrapper.HydrodynamicsLawLBM.dict, yade.wrapper.CohFrictPhys.dict, yade.wrapper.Bo1_Polyhedra_Aabb.dict, yade.wrapper.Law2_ScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.IPhys.dict, yade.wrapper.GlobalStiffnessTimeStepper.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom6D.dict, yade.wrapper.Ip2_FrictMat_CpmMat_FrictPhys.dict, yade.wrapper.TetraVolumetricLaw.dict, yade.wrapper.KinemCNSEngine.dict, yade.wrapper.Gl1_GridConnection.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_HertzWithLinearShear.dict, yade.wrapper.GridNodeGeom6D.dict, yade.wrapper.CohesiveDeformableElementMaterial.dict, yade.wrapper.KinemSimpleShearBox.dict, yade.wrapper.Law2_L6Geom_FrictPhys_Linear.dict, yade.wrapper.L6Geom.dict, yade.wrapper.GlIPhysDispatcher.dict, yade.wrapper.CohFrictMat.dict, yade.wrapper.Bo1_PFacet_Aabb.dict, yade.wrapper.SumIntrForcesCb.dict, yade.wrapper.MindlinPhys.dict, yade.wrapper.Ip2_2xInelastCohFrictMat_InelastCohFrictPhys.dict, yade.wrapper.CpmStateUpdater.dict, yade.wrapper.Tetra.dict, yade.wrapper.Gl1_PolyhedraPhys.dict, yade.wrapper.HelixEngine.dict, yade.wrapper.ThreeDTriaxialEngine.dict, yade.wrapper.JCFpmState.dict, yade.wrapper.Bo1_Tetra_Aabb.dict, yade.wrapper.Law2_ScGeom_MortarPhys_Lourenco.dict, yade.wrapper.Ig2_Sphere_Sphere_L3Geom.dict, yade.wrapper.Box.dict, yade.wrapper.PolyhedraSplitter.dict, yade.wrapper.LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.TimeStepper.dict, yade.wrapper.Gl1_Box.dict, yade.wrapper.Gl1_Tetra.dict, yade.wrapper.TriaxialTest.dict, yade.wrapper.PeriTriaxController.dict, yade.wrapper.InternalForceFunctor.dict, yade.wrapper.AxialGravityEngine.dict, yade.wrapper.Gl1_PolyhedraGeom.dict, yade.wrapper.VTKRecorder.dict, yade.wrapper.Bo1_ChainedCylinder_Aabb.dict, yade.wrapper.Ip2_2xNormalInelasticMat_NormalInelasticityPhys.dict, yade.wrapper.Bound.dict, yade.wrapper.BubbleMat.dict, yade.wrapper.KinematicEngine.dict, yade.wrapper.RotationEngine.dict, yade.wrapper.ResetRandomPosition.dict, yade.wrapper.Ip2_CpmMat_CpmMat_CpmPhys.dict, yade.wrapper.FrictPhys.dict, yade.wrapper.Law2_ScGeom_BubblePhys_Bubble.dict, yade.wrapper.FieldApplier.dict, yade.wrapper.Gl1_CpmPhys.dict, yade.wrapper.PeriodicEngine.dict, yade.wrapper.NormPhys.dict, yade.wrapper.GenericSpheresContact.dict, yade.wrapper.BicyclePedalEngine.dict, yade.wrapper.TTetraSimpleGeom.dict, yade.wrapper.Body.dict, yade.wrapper.WirePhys.dict, yade.wrapper.Gl1_PFacet.dict, yade.wrapper.Interaction.dict, yade.wrapper.DeformableCohesiveElement.dict, yade.wrapper.TTetraGeom.dict, yade.wrapper.CohesiveFrictionalContactLaw.dict, yade.wrapper.Law2_CylScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.Collider.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_ScGeom.dict, yade.wrapper.Node.dict, yade.wrapper.PeriIsoCompressor.dict, yade.wrapper.LBMnode.dict, yade.wrapper.FrictViscoMat.dict, yade.wrapper.MicroMacroAnalyser.dict, yade.wrapper.Material.dict, yade.wrapper.GlBoundDispatcher.dict, yade.wrapper.Law2_ScGeom_ViscoFrictPhys_CundallStrack.dict, yade.wrapper.GridConnection.dict, yade.wrapper.GlExtra_OctreeCubes.dict, yade.wrapper.Gl1_Cylinder.dict, yade.wrapper.Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys.dict, yade.wrapper.Law2_ScGeom_FrictViscoPhys_CundallStrackVisco.dict, yade.wrapper.GlStateDispatcher.dict, yade.wrapper.Shape.dict, yade.wrapper.OpenGLRenderer.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormShearPhys.dict, yade.wrapper.ChCylGeom6D.dict, yade.wrapper.PolyhedraGeom.dict, yade.wrapper.Ig2_Facet_Polyhedra_PolyhedraGeom.dict, yade.wrapper.NormalInelasticityPhys.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraSimpleGeom.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom.dict, yade.wrapper.CapillaryPhys.dict, yade.wrapper.LawTester.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom.dict, yade.wrapper.ViscoFrictPhys.dict, yade.wrapper.GlobalEngine.dict, yade.wrapper.Gl1_NormPhys.dict, yade.wrapper.Clump.dict, yade.wrapper.IPhysFunctor.dict, yade.wrapper.Cylinder.dict, yade.wrapper.Ig2_GridNode_GridNode_GridNodeGeom6D.dict, yade.wrapper.SnapshotEngine.dict, yade.wrapper.TorqueRecorder.dict, yade.wrapper.ParallelEngine.dict, yade.wrapper.InelastCohFrictPhys.dict, yade.wrapper.Bo1_Box_Aabb.dict, yade.wrapper.FlowEngineT.dict, yade.wrapper.Ip2_ViscElMat_ViscElMat_ViscElPhys.dict, yade.wrapper.PersistentTriangulationCollider.dict, yade.wrapper.Bo1_Wall_Aabb.dict, yade.wrapper.Ig2_Wall_Sphere_L3Geom.dict, yade.wrapper.TriaxialStateRecorder.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom.dict, yade.wrapper.Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.MortarMat.dict, yade.wrapper.Ig2_Wall_PFacet_ScGeom.dict, yade.wrapper.LudingMat.dict, yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement.dict, yade.wrapper.Gl1_Node.dict, yade.wrapper.Ip2_FrictMat_FrictMat_ViscoFrictPhys.dict, yade.wrapper.ZECollider.dict, yade.wrapper.Ip2_MortarMat_MortarMat_MortarPhys.dict, yade.wrapper.IntrCallback.dict, yade.wrapper.TesselationWrapper.dict, yade.wrapper.StepDisplacer.dict, yade.wrapper.ElasticContactLaw.dict, yade.wrapper.GlShapeDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys.dict, yade.wrapper.Lin4NodeTetra.dict, yade.wrapper.IGeom.dict, yade.wrapper.Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D.dict, yade.wrapper.Dispatcher.dict, yade.wrapper.CombinedKinematicEngine.dict, yade.wrapper.LBMlink.dict, yade.wrapper.Law2_ScGeom_LudingPhys_Basic.dict, yade.wrapper.Ip2_WireMat_WireMat_WirePhys.dict, yade.wrapper.Law2_ScGeom_ViscElCapPhys_Basic.dict, yade.wrapper.SimpleShear.dict, yade.wrapper.Bo1_Sphere_Aabb.dict, yade.wrapper.Engine.dict, yade.wrapper.ScGeom6D.dict, yade.wrapper.LudingPhys.dict, yade.wrapper.LBMbody.dict, yade.wrapper.KinemCNLEngine.dict, yade.wrapper.KinemCNDEngine.dict, yade.wrapper.WireState.dict, yade.wrapper.DragEngine.dict, yade.wrapper.CircularFactory.dict, yade.wrapper.Gl1_Sphere.dict, yade.wrapper.Scene.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormPhys.dict, yade.wrapper.Gl1_Aabb.dict, yade.wrapper.GlShapeFunctor.dict, yade.wrapper.Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys.dict, yade.wrapper.TriaxialStressController.dict, yade.wrapper.ChainedState.dict, yade.wrapper.Law2_GridCoGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HarmonicMotionEngine.dict, yade.wrapper.Law2_ScGridCoGeom_CohFrictPhys_CundallStrack.dict, yade.wrapper.RadialForceEngine.dict, yade.wrapper.Functor.dict, yade.wrapper.GeneralIntegratorInsertionSortCollider.dict, yade.wrapper.ScGridCoGeom.dict, yade.wrapper.IGeomDispatcher.dict, yade.wrapper.ElastMat.dict, yade.wrapper.Law2_ScGeom_ViscElPhys_Basic.dict, yade.wrapper.MatchMaker.dict, yade.wrapper.ServoPIDController.dict, yade.wrapper.GlIGeomFunctor.dict, yade.wrapper.Law2_CylScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HdapsGravityEngine.dict, yade.wrapper.CylScGeom6D.dict, yade.wrapper.Ig2_Sphere_GridConnection_ScGridCoGeom.dict, yade.wrapper.Cell.dict, yade.wrapper.JCFpmPhys.dict, yade.wrapper.WireMat.dict, yade.wrapper.Serializable.dict, yade.wrapper.NormShearPhys.dict, yade.wrapper.SpheresFactory.dict, yade.wrapper.Law2_ScGeom_CpmPhys_Cpm.dict, yade.wrapper.Bo1_Facet_Aabb.dict, yade.wrapper.GravityEngine.dict, yade.wrapper.Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.KinemCTDEngine.dict, yade.wrapper.BubblePhys.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinPhys.dict, yade.wrapper.BoundDispatcher.dict, yade.wrapper.InterpolatingHelixEngine.dict, yade.wrapper.Law2_ScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.Bo1_GridConnection_Aabb.dict, yade.wrapper.Ip2_BubbleMat_BubbleMat_BubblePhys.dict, yade.wrapper.BoundFunctor.dict, yade.wrapper.Bo1_Cylinder_Aabb.dict, yade.wrapper.Law2_TTetraSimpleGeom_NormPhys_Simple.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom.dict, yade.wrapper.Integrator.dict, yade.wrapper.MindlinCapillaryPhys.dict, yade.wrapper.Gl1_Polyhedra.dict, yade.wrapper.IPhysDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictMat_FrictPhys.dict, yade.wrapper.If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.NormalInelasticMat.dict, yade.wrapper.FacetTopologyAnalyzer.dict, yade.wrapper.GlIPhysFunctor.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.dict, yade.wrapper.SpatialQuickSortCollider.dict, yade.wrapper.Gl1_L3Geom.dict, yade.wrapper.PeriodicFlowEngine.dict, yade.wrapper.Law2_L3Geom_FrictPhys_ElPerfPl.dict, yade.wrapper.TriaxialCompressionEngine.dict, yade.wrapper.Disp2DPropLoadEngine.dict, yade.wrapper.JCFpmMat.dict, yade.wrapper.PolyhedraMat.dict, yade.wrapper.RungeKuttaCashKarp54Integrator.dict, yade.wrapper.GlStateFunctor.dict, yade.wrapper.Bo1_DeformableElement_Aabb.dict, yade.wrapper.BoundaryController.dict, yade.wrapper.TranslationEngine.dict, yade.wrapper.InelastCohFrictMat.dict, yade.wrapper.Law2_ScGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.DeformableElementMaterial.dict, yade.wrapper.GlIGeomDispatcher.dict, yade.wrapper.TorqueEngine.dict, yade.wrapper.FrictViscoPhys.dict, yade.wrapper.Recorder.dict, yade.wrapper.ChainedCylinder.dict, yade.wrapper.Polyhedra.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraGeom.dict, yade.wrapper.FEInternalForceEngine.dict, yade.wrapper.Ip2_FrictMat_PolyhedraMat_FrictPhys.dict, yade.wrapper.Gl1_Wall.dict, yade.wrapper.CpmMat.dict, yade.wrapper.LawFunctor.dict, yade.wrapper.CpmState.dict, yade.wrapper.Sphere.dict, yade.wrapper.LinCohesiveElasticMaterial.dict, yade.wrapper.Gl1_L6Geom.dict, yade.wrapper.LinIsoRayleighDampElastMat.dict, yade.wrapper.BoxFactory.dict, yade.wrapper.Law2_ScGeom_CapillaryPhys_Capillarity.dict, yade.wrapper.Ig2_Wall_Polyhedra_PolyhedraGeom.dict, yade.wrapper.FlowEngine.dict, yade.wrapper.Wall.dict, yade.wrapper.PolyhedraPhys.dict, yade.wrapper.Gl1_DeformableElement.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom6D.dict, yade.wrapper.InteractionLoop.dict, yade.wrapper.Ig2_Sphere_PFacet_ScGridCoGeom.dict, yade.wrapper.CapillaryTriaxialTest.dict, yade.wrapper.MortarPhys.dict, yade.wrapper.Gl1_Facet.dict, yade.wrapper.PyRunner.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom6D.dict, yade.wrapper.CentralGravityEngine.dict, yade.wrapper.UniaxialStrainer.dict, yade.wrapper.FrictMat.dict, yade.wrapper.CylScGeom.dict, yade.wrapper.GlExtra_LawTester.dict, yade.wrapper.Law2_ScGeom_WirePhys_WirePM.dict, yade.wrapper.InternalForceDispatcher.dict, yade.wrapper.Ig2_Sphere_Sphere_L6Geom.dict, yade.wrapper.Law2_PolyhedraGeom_PolyhedraPhys_Volumetric.dict, yade.wrapper.GridNode.dict, yade.wrapper.FileGenerator.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom6D.dict, yade.wrapper.Ig2_PFacet_PFacet_ScGeom.dict, yade.wrapper.CpmPhys.dict, yade.wrapper.Ig2_Facet_Sphere_L3Geom.dict, yade.wrapper.ForceResetter.dict, yade.wrapper.Ip2_FrictMat_FrictMat_CapillaryPhys.dict, yade.wrapper.ViscElPhys.dict, yade.wrapper.EnergyTracker.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom.dict, yade.wrapper.Ig2_GridConnection_GridConnection_GridCoGridCoGeom.dict, yade.wrapper.Aabb.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_MindlinDeresiewitz.dict, yade.wrapper.GlBoundFunctor.dict, yade.wrapper.State.dict, yade.wrapper.ScGeom.dict, yade.wrapper.Peri3dController.dict, yade.wrapper.InterpolatingDirectedForceEngine.dict, yade.wrapper.ForceRecorder.dict, yade.wrapper.Ig2_GridConnection_PFacet_ScGeom.dict, yade.wrapper.PartialEngine.dict, yade.wrapper.ViscElCapPhys.dict, yade.wrapper.L3Geom.dict, yade.wrapper.FlatGridCollider.dict, yade.wrapper.DeformableElement.dict, yade.wrapper.Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.dict, yade.wrapper.Ip2_LudingMat_LudingMat_LudingPhys.dict, yade.wrapper.LinIsoElastMat.dict, yade.wrapper.HarmonicRotationEngine.dict, yade.wrapper.Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity.dict, yade.wrapper.ForceEngine.dict, yade.wrapper.Bo1_Node_Aabb.dict, yade.wrapper.Ig2_Sphere_Polyhedra_ScGeom.dict, yade.wrapper.IGeomFunctor.dict, yade.wrapper.Ig2_Wall_Sphere_ScGeom.dict, yade.wrapper.DomainLimiter.dict, yade.wrapper.Gl1_ChainedCylinder.dict, yade.wrapper.If2_Lin4NodeTetra_LinIsoRayleighDampElast.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeom.dict, yade.wrapper.GlExtraDrawer.dict, yade.wrapper.HydroForceEngine.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_Mindlin.dict
docstring of yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys:1: WARNING: citation not found: Duriez2016
generating indices... genindex py-modindex
highlighting module code... [ 10%] Law2_ScGeom6D_InelastCohFrictPhys_CohesionMomhighlighting module code... [100%] yade._packSpheres
writing additional pages... index search
copying images... [100%] fig/simple-scene-plot-3.png
copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 16 warnings.
Running Sphinx v1.3.6
WARNING: the config value 'my_maketitle' is set to a string with non-ASCII characters; this can lead to Unicode errors occurring. Please use Unicode strings, e.g. u'Content'.
WARNING: extension 'youtube' has no setup() function; is it really a Sphinx extension module?
building [mo]: all of 0 po files
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updating environment: 39 added, 0 changed, 0 removed
reading sources... [ 33%] introduction

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 321
Specify :okexcept: as an option in the ipython:: block to suppress this message
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IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies[100]

IndexError: Body id out of range.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 327
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies.append(s)

IndexError: Body already has id 0 set; appending such body (for the second time) is not allowed.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 382
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.interactions[100,10111]

IndexError: No such interaction
<<<-------------------------------------------------------------------------

reading sources... [ 38%] prog

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 434
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 Sphere().name ## getClassName()

AttributeError: 'Sphere' object has no attribute 'name'
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1466
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.forces.f(100)

IndexError: Body id out of range.
<<<-------------------------------------------------------------------------

reading sources... [ 58%] tutorial-hands-on

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 197
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 a[3] # error

IndexError: list index out of range
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 226
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 b[0]=4 # error

TypeError: 'tuple' object does not support item assignment
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 383
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies[1].shape.radius # radius of body #1 (will give error if not sphere, since only spheres have radius defined)

AttributeError: 'NoneType' object has no attribute 'shape'
<<<-------------------------------------------------------------------------

ERROR /home/hjz/yade2017/trunk/pkg/common/InsertionSortCollider.cpp:240 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.
reading sources... [100%] yade.ymport
/home/hjz/yade2017/build/doc/sphinx/index-toctree-manuals.rst:6: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/index-toctree-reference.rst:5: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/index-toctree-theory.rst:5: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/publications.rst:127: WARNING: Inline emphasis start-string without end-string.
/home/hjz/yade2017/build/doc/sphinx/publications.rst:429: WARNING: Duplicate explicit target name: "maurin2015".
/home/hjz/yade2017/build/doc/sphinx/publications.rst:429: WARNING: duplicate citation Maurin2015, other instance in /home/hjz/yade2017/build/doc/sphinx/publications.rst
/home/hjz/yade2017/build/doc/sphinx/yade.wrapper.rst:1: WARNING: malformed hyperlink target.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/hjz/yade2017/build/doc/sphinx/consulting.rst:: WARNING: document isn't included in any toctree
/home/hjz/yade2017/build/doc/sphinx/index-toctree-book.rst:: WARNING: document isn't included in any toctree
/home/hjz/yade2017/build/doc/sphinx/index-toctree_manuals.rst:: WARNING: document isn't included in any toctree
done
processing Yade.tex... index-toctree introduction tutorial tutorial-introduction tutorial-hands-on tutorial-data-mining tutorial-geo tutorial-advanced tutorial-examples user prog installation github formulation yade.wrapper modules yade.bodiesHandling yade.export yade.geom yade.gridpfacet yade.linterpolation yade.pack yade.plot yade.polyhedra_utils yade.post2d yade.qt yade.timing yade.utils yade.ymport FEMxDEM citing publications references
resolving references...
docstring of yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys:1: WARNING: citation not found: Duriez2016
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:docstring of yade.utils.UnstructuredGrid:None: WARNING: more than one target found for cross-reference u'dict': yade.wrapper.Facet.dict, yade.wrapper.InsertionSortCollider.dict, yade.wrapper.ViscElCapMat.dict, yade.wrapper.LinearDragEngine.dict, yade.wrapper.Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.dict, yade.wrapper.CapillaryStressRecorder.dict, yade.wrapper.PFacet.dict, yade.wrapper.LawDispatcher.dict, yade.wrapper.FlowEngine_PeriodicInfo.dict, yade.wrapper.GridCoGridCoGeom.dict, yade.wrapper.CohesiveTriaxialTest.dict, yade.wrapper.NewtonIntegrator.dict, yade.wrapper.ViscElMat.dict, yade.wrapper.HydrodynamicsLawLBM.dict, yade.wrapper.CohFrictPhys.dict, yade.wrapper.Bo1_Polyhedra_Aabb.dict, yade.wrapper.IPhys.dict, yade.wrapper.GlobalStiffnessTimeStepper.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom6D.dict, yade.wrapper.Ip2_FrictMat_CpmMat_FrictPhys.dict, yade.wrapper.TetraVolumetricLaw.dict, yade.wrapper.KinemCNSEngine.dict, yade.wrapper.Gl1_GridConnection.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_HertzWithLinearShear.dict, yade.wrapper.GridNodeGeom6D.dict, yade.wrapper.CohesiveDeformableElementMaterial.dict, yade.wrapper.KinemSimpleShearBox.dict, yade.wrapper.Law2_L6Geom_FrictPhys_Linear.dict, yade.wrapper.L6Geom.dict, yade.wrapper.GlIPhysDispatcher.dict, yade.wrapper.CohFrictMat.dict, yade.wrapper.Bo1_PFacet_Aabb.dict, yade.wrapper.SumIntrForcesCb.dict, yade.wrapper.MindlinPhys.dict, yade.wrapper.Ip2_2xInelastCohFrictMat_InelastCohFrictPhys.dict, yade.wrapper.CpmStateUpdater.dict, yade.wrapper.Tetra.dict, yade.wrapper.Gl1_PolyhedraPhys.dict, yade.wrapper.ThreeDTriaxialEngine.dict, yade.wrapper.JCFpmState.dict, yade.wrapper.Bo1_Tetra_Aabb.dict, yade.wrapper.RungeKuttaCashKarp54Integrator.dict, yade.wrapper.Law2_ScGeom_MortarPhys_Lourenco.dict, yade.wrapper.Ig2_Sphere_Sphere_L3Geom.dict, yade.wrapper.Box.dict, yade.wrapper.PolyhedraSplitter.dict, yade.wrapper.LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.TimeStepper.dict, yade.wrapper.Gl1_Box.dict, yade.wrapper.ForceResetter.dict, yade.wrapper.Gl1_Tetra.dict, yade.wrapper.TriaxialTest.dict, yade.wrapper.PeriTriaxController.dict, yade.wrapper.PeriodicEngine.dict, yade.wrapper.InternalForceFunctor.dict, yade.wrapper.Gl1_PolyhedraGeom.dict, yade.wrapper.VTKRecorder.dict, yade.wrapper.Bo1_ChainedCylinder_Aabb.dict, yade.wrapper.Ip2_2xNormalInelasticMat_NormalInelasticityPhys.dict, yade.wrapper.Bound.dict, yade.wrapper.BubbleMat.dict, yade.wrapper.KinematicEngine.dict, yade.wrapper.RotationEngine.dict, yade.wrapper.ResetRandomPosition.dict, yade.wrapper.Law2_ScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_CylScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.FrictPhys.dict, yade.wrapper.Law2_ScGeom_BubblePhys_Bubble.dict, yade.wrapper.Gl1_CpmPhys.dict, yade.wrapper.GlobalEngine.dict, yade.wrapper.AxialGravityEngine.dict, yade.wrapper.NormPhys.dict, yade.wrapper.GenericSpheresContact.dict, yade.wrapper.BicyclePedalEngine.dict, yade.wrapper.TTetraSimpleGeom.dict, yade.wrapper.Body.dict, yade.wrapper.WirePhys.dict, yade.wrapper.Gl1_PFacet.dict, yade.wrapper.Interaction.dict, yade.wrapper.DeformableCohesiveElement.dict, yade.wrapper.TTetraGeom.dict, yade.wrapper.CohesiveFrictionalContactLaw.dict, yade.wrapper.Collider.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_ScGeom.dict, yade.wrapper.Ip2_ViscElMat_ViscElMat_ViscElPhys.dict, yade.wrapper.Node.dict, yade.wrapper.PeriIsoCompressor.dict, yade.wrapper.LBMnode.dict, yade.wrapper.FrictViscoMat.dict, yade.wrapper.MicroMacroAnalyser.dict, yade.wrapper.Material.dict, yade.wrapper.GlBoundDispatcher.dict, yade.wrapper.Law2_ScGeom_ViscoFrictPhys_CundallStrack.dict, yade.wrapper.GridConnection.dict, yade.wrapper.GlExtra_OctreeCubes.dict, yade.wrapper.Gl1_Cylinder.dict, yade.wrapper.Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys.dict, yade.wrapper.Law2_ScGeom_FrictViscoPhys_CundallStrackVisco.dict, yade.wrapper.GlStateDispatcher.dict, yade.wrapper.Shape.dict, yade.wrapper.OpenGLRenderer.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormShearPhys.dict, yade.wrapper.ChCylGeom6D.dict, yade.wrapper.PolyhedraGeom.dict, yade.wrapper.Ig2_Facet_Polyhedra_PolyhedraGeom.dict, yade.wrapper.NormalInelasticityPhys.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraSimpleGeom.dict, yade.wrapper.HelixEngine.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom.dict, yade.wrapper.CapillaryPhys.dict, yade.wrapper.LawTester.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom.dict, yade.wrapper.ViscoFrictPhys.dict, yade.wrapper.Gl1_NormPhys.dict, yade.wrapper.Clump.dict, yade.wrapper.IPhysFunctor.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom.dict, yade.wrapper.Cylinder.dict, yade.wrapper.Ig2_GridNode_GridNode_GridNodeGeom6D.dict, yade.wrapper.SnapshotEngine.dict, yade.wrapper.TorqueRecorder.dict, yade.wrapper.ParallelEngine.dict, yade.wrapper.InelastCohFrictPhys.dict, yade.wrapper.Bo1_Box_Aabb.dict, yade.wrapper.FlowEngineT.dict, yade.wrapper.WireMat.dict, yade.wrapper.PersistentTriangulationCollider.dict, yade.wrapper.Integrator.dict, yade.wrapper.Bo1_Wall_Aabb.dict, yade.wrapper.TriaxialStateRecorder.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom.dict, yade.wrapper.Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.MortarMat.dict, yade.wrapper.Ig2_Wall_PFacet_ScGeom.dict, yade.wrapper.LudingMat.dict, yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement.dict, yade.wrapper.Gl1_Node.dict, yade.wrapper.Ip2_FrictMat_FrictMat_ViscoFrictPhys.dict, yade.wrapper.Ip2_MortarMat_MortarMat_MortarPhys.dict, yade.wrapper.IntrCallback.dict, yade.wrapper.TesselationWrapper.dict, yade.wrapper.StepDisplacer.dict, yade.wrapper.ElasticContactLaw.dict, yade.wrapper.GlShapeDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys.dict, yade.wrapper.Lin4NodeTetra.dict, yade.wrapper.IGeom.dict, yade.wrapper.Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D.dict, yade.wrapper.Dispatcher.dict, yade.wrapper.CombinedKinematicEngine.dict, yade.wrapper.LBMlink.dict, yade.wrapper.Law2_ScGeom_LudingPhys_Basic.dict, yade.wrapper.Ip2_WireMat_WireMat_WirePhys.dict, yade.wrapper.Law2_ScGeom_ViscElCapPhys_Basic.dict, yade.wrapper.SimpleShear.dict, yade.wrapper.Bo1_Sphere_Aabb.dict, yade.wrapper.Engine.dict, yade.wrapper.ScGeom6D.dict, yade.wrapper.LudingPhys.dict, yade.wrapper.LBMbody.dict, yade.wrapper.KinemCNLEngine.dict, yade.wrapper.KinemCNDEngine.dict, yade.wrapper.WireState.dict, yade.wrapper.DragEngine.dict, yade.wrapper.CircularFactory.dict, yade.wrapper.Gl1_Sphere.dict, yade.wrapper.Scene.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormPhys.dict, yade.wrapper.Gl1_Aabb.dict, yade.wrapper.GlShapeFunctor.dict, yade.wrapper.Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys.dict, yade.wrapper.TriaxialStressController.dict, yade.wrapper.Ig2_Wall_Sphere_L3Geom.dict, yade.wrapper.ChainedState.dict, yade.wrapper.Law2_GridCoGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HarmonicMotionEngine.dict, yade.wrapper.Law2_ScGridCoGeom_CohFrictPhys_CundallStrack.dict, yade.wrapper.RadialForceEngine.dict, yade.wrapper.Functor.dict, yade.wrapper.GeneralIntegratorInsertionSortCollider.dict, yade.wrapper.ScGridCoGeom.dict, yade.wrapper.IGeomDispatcher.dict, yade.wrapper.ElastMat.dict, yade.wrapper.Law2_ScGeom_ViscElPhys_Basic.dict, yade.wrapper.MatchMaker.dict, yade.wrapper.ServoPIDController.dict, yade.wrapper.GlIGeomFunctor.dict, yade.wrapper.L3Geom.dict, yade.wrapper.Law2_CylScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HdapsGravityEngine.dict, yade.wrapper.CylScGeom6D.dict, yade.wrapper.Ig2_Sphere_GridConnection_ScGridCoGeom.dict, yade.wrapper.Cell.dict, yade.wrapper.JCFpmPhys.dict, yade.wrapper.NormShearPhys.dict, yade.wrapper.SpheresFactory.dict, yade.wrapper.Law2_ScGeom_CpmPhys_Cpm.dict, yade.wrapper.Bo1_Facet_Aabb.dict, yade.wrapper.GravityEngine.dict, yade.wrapper.Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.KinemCTDEngine.dict, yade.wrapper.BubblePhys.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinPhys.dict, yade.wrapper.BoundDispatcher.dict, yade.wrapper.InterpolatingHelixEngine.dict, yade.wrapper.Law2_ScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.Bo1_GridConnection_Aabb.dict, yade.wrapper.Ip2_BubbleMat_BubbleMat_BubblePhys.dict, yade.wrapper.BoundFunctor.dict, yade.wrapper.Bo1_Cylinder_Aabb.dict, yade.wrapper.Law2_TTetraSimpleGeom_NormPhys_Simple.dict, yade.wrapper.MindlinCapillaryPhys.dict, yade.wrapper.Gl1_Polyhedra.dict, yade.wrapper.IPhysDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictMat_FrictPhys.dict, yade.wrapper.If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.NormalInelasticMat.dict, yade.wrapper.FacetTopologyAnalyzer.dict, yade.wrapper.GlIPhysFunctor.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.dict, yade.wrapper.SpatialQuickSortCollider.dict, yade.wrapper.Gl1_L3Geom.dict, yade.wrapper.PeriodicFlowEngine.dict, yade.wrapper.Ip2_CpmMat_CpmMat_CpmPhys.dict, yade.wrapper.Law2_L3Geom_FrictPhys_ElPerfPl.dict, yade.wrapper.TriaxialCompressionEngine.dict, yade.wrapper.Disp2DPropLoadEngine.dict, yade.wrapper.JCFpmMat.dict, yade.wrapper.PolyhedraMat.dict, yade.wrapper.Serializable.dict, yade.wrapper.GlStateFunctor.dict, yade.wrapper.Bo1_DeformableElement_Aabb.dict, yade.wrapper.BoundaryController.dict, yade.wrapper.TranslationEngine.dict, yade.wrapper.InelastCohFrictMat.dict, yade.wrapper.Law2_ScGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.DeformableElementMaterial.dict, yade.wrapper.GlIGeomDispatcher.dict, yade.wrapper.ZECollider.dict, yade.wrapper.TorqueEngine.dict, yade.wrapper.FrictViscoPhys.dict, yade.wrapper.Recorder.dict, yade.wrapper.ChainedCylinder.dict, yade.wrapper.Polyhedra.dict, yade.wrapper.ForceEngine.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraGeom.dict, yade.wrapper.FEInternalForceEngine.dict, yade.wrapper.Ip2_FrictMat_PolyhedraMat_FrictPhys.dict, yade.wrapper.Gl1_Wall.dict, yade.wrapper.LawFunctor.dict, yade.wrapper.CpmState.dict, yade.wrapper.Sphere.dict, yade.wrapper.Bo1_Node_Aabb.dict, yade.wrapper.LinCohesiveElasticMaterial.dict, yade.wrapper.Gl1_L6Geom.dict, yade.wrapper.LinIsoRayleighDampElastMat.dict, yade.wrapper.BoxFactory.dict, yade.wrapper.Law2_ScGeom_CapillaryPhys_Capillarity.dict, yade.wrapper.CpmMat.dict, yade.wrapper.Ig2_Wall_Polyhedra_PolyhedraGeom.dict, yade.wrapper.FlowEngine.dict, yade.wrapper.Wall.dict, yade.wrapper.PolyhedraPhys.dict, yade.wrapper.Gl1_DeformableElement.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom6D.dict, yade.wrapper.InteractionLoop.dict, yade.wrapper.Ig2_Sphere_PFacet_ScGridCoGeom.dict, yade.wrapper.Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.dict, yade.wrapper.MortarPhys.dict, yade.wrapper.Gl1_Facet.dict, yade.wrapper.PyRunner.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom6D.dict, yade.wrapper.CentralGravityEngine.dict, yade.wrapper.UniaxialStrainer.dict, yade.wrapper.FrictMat.dict, yade.wrapper.CylScGeom.dict, yade.wrapper.GlExtra_LawTester.dict, yade.wrapper.Law2_ScGeom_WirePhys_WirePM.dict, yade.wrapper.InternalForceDispatcher.dict, yade.wrapper.Ig2_Sphere_Sphere_L6Geom.dict, yade.wrapper.Law2_PolyhedraGeom_PolyhedraPhys_Volumetric.dict, yade.wrapper.GridNode.dict, yade.wrapper.FileGenerator.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom6D.dict, yade.wrapper.Ig2_PFacet_PFacet_ScGeom.dict, yade.wrapper.CpmPhys.dict, yade.wrapper.Ig2_Facet_Sphere_L3Geom.dict, yade.wrapper.Ip2_FrictMat_FrictMat_CapillaryPhys.dict, yade.wrapper.ViscElPhys.dict, yade.wrapper.EnergyTracker.dict, yade.wrapper.Ig2_GridConnection_GridConnection_GridCoGridCoGeom.dict, yade.wrapper.Aabb.dict, yade.wrapper.FieldApplier.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_MindlinDeresiewitz.dict, yade.wrapper.GlBoundFunctor.dict, yade.wrapper.State.dict, yade.wrapper.ScGeom.dict, yade.wrapper.Peri3dController.dict, yade.wrapper.InterpolatingDirectedForceEngine.dict, yade.wrapper.ForceRecorder.dict, yade.wrapper.Ig2_GridConnection_PFacet_ScGeom.dict, yade.wrapper.PartialEngine.dict, yade.wrapper.ViscElCapPhys.dict, yade.wrapper.FlatGridCollider.dict, yade.wrapper.DeformableElement.dict, yade.wrapper.CapillaryTriaxialTest.dict, yade.wrapper.Ip2_LudingMat_LudingMat_LudingPhys.dict, yade.wrapper.LinIsoElastMat.dict, yade.wrapper.HarmonicRotationEngine.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom.dict, yade.wrapper.Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_Mindlin.dict, yade.wrapper.Ig2_Sphere_Polyhedra_ScGeom.dict, yade.wrapper.IGeomFunctor.dict, yade.wrapper.Ig2_Wall_Sphere_ScGeom.dict, yade.wrapper.DomainLimiter.dict, yade.wrapper.Gl1_ChainedCylinder.dict, yade.wrapper.If2_Lin4NodeTetra_LinIsoRayleighDampElast.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeom.dict, yade.wrapper.GlExtraDrawer.dict, yade.wrapper.HydroForceEngine.dict
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:docstring of yade.utils.UnstructuredGrid:None: WARNING: more than one target found for cross-reference u'dict': yade.wrapper.Facet.dict, yade.wrapper.InsertionSortCollider.dict, yade.wrapper.ViscElCapMat.dict, yade.wrapper.LinearDragEngine.dict, yade.wrapper.Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.dict, yade.wrapper.CapillaryStressRecorder.dict, yade.wrapper.PFacet.dict, yade.wrapper.LawDispatcher.dict, yade.wrapper.FlowEngine_PeriodicInfo.dict, yade.wrapper.GridCoGridCoGeom.dict, yade.wrapper.CohesiveTriaxialTest.dict, yade.wrapper.NewtonIntegrator.dict, yade.wrapper.ViscElMat.dict, yade.wrapper.HydrodynamicsLawLBM.dict, yade.wrapper.CohFrictPhys.dict, yade.wrapper.Bo1_Polyhedra_Aabb.dict, yade.wrapper.IPhys.dict, yade.wrapper.GlobalStiffnessTimeStepper.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom6D.dict, yade.wrapper.Ip2_FrictMat_CpmMat_FrictPhys.dict, yade.wrapper.TetraVolumetricLaw.dict, yade.wrapper.KinemCNSEngine.dict, yade.wrapper.Gl1_GridConnection.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_HertzWithLinearShear.dict, yade.wrapper.GridNodeGeom6D.dict, yade.wrapper.CohesiveDeformableElementMaterial.dict, yade.wrapper.KinemSimpleShearBox.dict, yade.wrapper.Law2_L6Geom_FrictPhys_Linear.dict, yade.wrapper.L6Geom.dict, yade.wrapper.GlIPhysDispatcher.dict, yade.wrapper.CohFrictMat.dict, yade.wrapper.Bo1_PFacet_Aabb.dict, yade.wrapper.SumIntrForcesCb.dict, yade.wrapper.MindlinPhys.dict, yade.wrapper.Ip2_2xInelastCohFrictMat_InelastCohFrictPhys.dict, yade.wrapper.CpmStateUpdater.dict, yade.wrapper.Tetra.dict, yade.wrapper.Gl1_PolyhedraPhys.dict, yade.wrapper.ThreeDTriaxialEngine.dict, yade.wrapper.JCFpmState.dict, yade.wrapper.Bo1_Tetra_Aabb.dict, yade.wrapper.RungeKuttaCashKarp54Integrator.dict, yade.wrapper.Law2_ScGeom_MortarPhys_Lourenco.dict, yade.wrapper.Ig2_Sphere_Sphere_L3Geom.dict, yade.wrapper.Box.dict, yade.wrapper.PolyhedraSplitter.dict, yade.wrapper.LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.TimeStepper.dict, yade.wrapper.Gl1_Box.dict, yade.wrapper.ForceResetter.dict, yade.wrapper.Gl1_Tetra.dict, yade.wrapper.TriaxialTest.dict, yade.wrapper.PeriTriaxController.dict, yade.wrapper.PeriodicEngine.dict, yade.wrapper.InternalForceFunctor.dict, yade.wrapper.Gl1_PolyhedraGeom.dict, yade.wrapper.VTKRecorder.dict, yade.wrapper.Bo1_ChainedCylinder_Aabb.dict, yade.wrapper.Ip2_2xNormalInelasticMat_NormalInelasticityPhys.dict, yade.wrapper.Bound.dict, yade.wrapper.BubbleMat.dict, yade.wrapper.KinematicEngine.dict, yade.wrapper.RotationEngine.dict, yade.wrapper.ResetRandomPosition.dict, yade.wrapper.Law2_ScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_CylScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.FrictPhys.dict, yade.wrapper.Law2_ScGeom_BubblePhys_Bubble.dict, yade.wrapper.Gl1_CpmPhys.dict, yade.wrapper.GlobalEngine.dict, yade.wrapper.AxialGravityEngine.dict, yade.wrapper.NormPhys.dict, yade.wrapper.GenericSpheresContact.dict, yade.wrapper.BicyclePedalEngine.dict, yade.wrapper.TTetraSimpleGeom.dict, yade.wrapper.Body.dict, yade.wrapper.WirePhys.dict, yade.wrapper.Gl1_PFacet.dict, yade.wrapper.Interaction.dict, yade.wrapper.DeformableCohesiveElement.dict, yade.wrapper.TTetraGeom.dict, yade.wrapper.CohesiveFrictionalContactLaw.dict, yade.wrapper.Collider.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_ScGeom.dict, yade.wrapper.Ip2_ViscElMat_ViscElMat_ViscElPhys.dict, yade.wrapper.Node.dict, yade.wrapper.PeriIsoCompressor.dict, yade.wrapper.LBMnode.dict, yade.wrapper.FrictViscoMat.dict, yade.wrapper.MicroMacroAnalyser.dict, yade.wrapper.Material.dict, yade.wrapper.GlBoundDispatcher.dict, yade.wrapper.Law2_ScGeom_ViscoFrictPhys_CundallStrack.dict, yade.wrapper.GridConnection.dict, yade.wrapper.GlExtra_OctreeCubes.dict, yade.wrapper.Gl1_Cylinder.dict, yade.wrapper.Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys.dict, yade.wrapper.Law2_ScGeom_FrictViscoPhys_CundallStrackVisco.dict, yade.wrapper.GlStateDispatcher.dict, yade.wrapper.Shape.dict, yade.wrapper.OpenGLRenderer.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormShearPhys.dict, yade.wrapper.ChCylGeom6D.dict, yade.wrapper.PolyhedraGeom.dict, yade.wrapper.Ig2_Facet_Polyhedra_PolyhedraGeom.dict, yade.wrapper.NormalInelasticityPhys.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraSimpleGeom.dict, yade.wrapper.HelixEngine.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom.dict, yade.wrapper.CapillaryPhys.dict, yade.wrapper.LawTester.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom.dict, yade.wrapper.ViscoFrictPhys.dict, yade.wrapper.Gl1_NormPhys.dict, yade.wrapper.Clump.dict, yade.wrapper.IPhysFunctor.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom.dict, yade.wrapper.Cylinder.dict, yade.wrapper.Ig2_GridNode_GridNode_GridNodeGeom6D.dict, yade.wrapper.SnapshotEngine.dict, yade.wrapper.TorqueRecorder.dict, yade.wrapper.ParallelEngine.dict, yade.wrapper.InelastCohFrictPhys.dict, yade.wrapper.Bo1_Box_Aabb.dict, yade.wrapper.FlowEngineT.dict, yade.wrapper.WireMat.dict, yade.wrapper.PersistentTriangulationCollider.dict, yade.wrapper.Integrator.dict, yade.wrapper.Bo1_Wall_Aabb.dict, yade.wrapper.TriaxialStateRecorder.dict, yade.wrapper.Ig2_Facet_Sphere_ScGeom.dict, yade.wrapper.Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.MortarMat.dict, yade.wrapper.Ig2_Wall_PFacet_ScGeom.dict, yade.wrapper.LudingMat.dict, yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement.dict, yade.wrapper.Gl1_Node.dict, yade.wrapper.Ip2_FrictMat_FrictMat_ViscoFrictPhys.dict, yade.wrapper.Ip2_MortarMat_MortarMat_MortarPhys.dict, yade.wrapper.IntrCallback.dict, yade.wrapper.TesselationWrapper.dict, yade.wrapper.StepDisplacer.dict, yade.wrapper.ElasticContactLaw.dict, yade.wrapper.GlShapeDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys.dict, yade.wrapper.Lin4NodeTetra.dict, yade.wrapper.IGeom.dict, yade.wrapper.Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D.dict, yade.wrapper.Dispatcher.dict, yade.wrapper.CombinedKinematicEngine.dict, yade.wrapper.LBMlink.dict, yade.wrapper.Law2_ScGeom_LudingPhys_Basic.dict, yade.wrapper.Ip2_WireMat_WireMat_WirePhys.dict, yade.wrapper.Law2_ScGeom_ViscElCapPhys_Basic.dict, yade.wrapper.SimpleShear.dict, yade.wrapper.Bo1_Sphere_Aabb.dict, yade.wrapper.Engine.dict, yade.wrapper.ScGeom6D.dict, yade.wrapper.LudingPhys.dict, yade.wrapper.LBMbody.dict, yade.wrapper.KinemCNLEngine.dict, yade.wrapper.KinemCNDEngine.dict, yade.wrapper.WireState.dict, yade.wrapper.DragEngine.dict, yade.wrapper.CircularFactory.dict, yade.wrapper.Gl1_Sphere.dict, yade.wrapper.Scene.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormPhys.dict, yade.wrapper.Gl1_Aabb.dict, yade.wrapper.GlShapeFunctor.dict, yade.wrapper.Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys.dict, yade.wrapper.TriaxialStressController.dict, yade.wrapper.Ig2_Wall_Sphere_L3Geom.dict, yade.wrapper.ChainedState.dict, yade.wrapper.Law2_GridCoGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HarmonicMotionEngine.dict, yade.wrapper.Law2_ScGridCoGeom_CohFrictPhys_CundallStrack.dict, yade.wrapper.RadialForceEngine.dict, yade.wrapper.Functor.dict, yade.wrapper.GeneralIntegratorInsertionSortCollider.dict, yade.wrapper.ScGridCoGeom.dict, yade.wrapper.IGeomDispatcher.dict, yade.wrapper.ElastMat.dict, yade.wrapper.Law2_ScGeom_ViscElPhys_Basic.dict, yade.wrapper.MatchMaker.dict, yade.wrapper.ServoPIDController.dict, yade.wrapper.GlIGeomFunctor.dict, yade.wrapper.L3Geom.dict, yade.wrapper.Law2_CylScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.HdapsGravityEngine.dict, yade.wrapper.CylScGeom6D.dict, yade.wrapper.Ig2_Sphere_GridConnection_ScGridCoGeom.dict, yade.wrapper.Cell.dict, yade.wrapper.JCFpmPhys.dict, yade.wrapper.NormShearPhys.dict, yade.wrapper.SpheresFactory.dict, yade.wrapper.Law2_ScGeom_CpmPhys_Cpm.dict, yade.wrapper.Bo1_Facet_Aabb.dict, yade.wrapper.GravityEngine.dict, yade.wrapper.Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.KinemCTDEngine.dict, yade.wrapper.BubblePhys.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinPhys.dict, yade.wrapper.BoundDispatcher.dict, yade.wrapper.InterpolatingHelixEngine.dict, yade.wrapper.Law2_ScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.Bo1_GridConnection_Aabb.dict, yade.wrapper.Ip2_BubbleMat_BubbleMat_BubblePhys.dict, yade.wrapper.BoundFunctor.dict, yade.wrapper.Bo1_Cylinder_Aabb.dict, yade.wrapper.Law2_TTetraSimpleGeom_NormPhys_Simple.dict, yade.wrapper.MindlinCapillaryPhys.dict, yade.wrapper.Gl1_Polyhedra.dict, yade.wrapper.IPhysDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictMat_FrictPhys.dict, yade.wrapper.If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.NormalInelasticMat.dict, yade.wrapper.FacetTopologyAnalyzer.dict, yade.wrapper.GlIPhysFunctor.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.dict, yade.wrapper.SpatialQuickSortCollider.dict, yade.wrapper.Gl1_L3Geom.dict, yade.wrapper.PeriodicFlowEngine.dict, yade.wrapper.Ip2_CpmMat_CpmMat_CpmPhys.dict, yade.wrapper.Law2_L3Geom_FrictPhys_ElPerfPl.dict, yade.wrapper.TriaxialCompressionEngine.dict, yade.wrapper.Disp2DPropLoadEngine.dict, yade.wrapper.JCFpmMat.dict, yade.wrapper.PolyhedraMat.dict, yade.wrapper.Serializable.dict, yade.wrapper.GlStateFunctor.dict, yade.wrapper.Bo1_DeformableElement_Aabb.dict, yade.wrapper.BoundaryController.dict, yade.wrapper.TranslationEngine.dict, yade.wrapper.InelastCohFrictMat.dict, yade.wrapper.Law2_ScGridCoGeom_FrictPhys_CundallStrack.dict, yade.wrapper.DeformableElementMaterial.dict, yade.wrapper.GlIGeomDispatcher.dict, yade.wrapper.ZECollider.dict, yade.wrapper.TorqueEngine.dict, yade.wrapper.FrictViscoPhys.dict, yade.wrapper.Recorder.dict, yade.wrapper.ChainedCylinder.dict, yade.wrapper.Polyhedra.dict, yade.wrapper.ForceEngine.dict, 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yade.wrapper.Ig2_Sphere_Sphere_ScGeom6D.dict, yade.wrapper.CentralGravityEngine.dict, yade.wrapper.UniaxialStrainer.dict, yade.wrapper.FrictMat.dict, yade.wrapper.CylScGeom.dict, yade.wrapper.GlExtra_LawTester.dict, yade.wrapper.Law2_ScGeom_WirePhys_WirePM.dict, yade.wrapper.InternalForceDispatcher.dict, yade.wrapper.Ig2_Sphere_Sphere_L6Geom.dict, yade.wrapper.Law2_PolyhedraGeom_PolyhedraPhys_Volumetric.dict, yade.wrapper.GridNode.dict, yade.wrapper.FileGenerator.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom6D.dict, yade.wrapper.Ig2_PFacet_PFacet_ScGeom.dict, yade.wrapper.CpmPhys.dict, yade.wrapper.Ig2_Facet_Sphere_L3Geom.dict, yade.wrapper.Ip2_FrictMat_FrictMat_CapillaryPhys.dict, yade.wrapper.ViscElPhys.dict, yade.wrapper.EnergyTracker.dict, yade.wrapper.Ig2_GridConnection_GridConnection_GridCoGridCoGeom.dict, yade.wrapper.Aabb.dict, yade.wrapper.FieldApplier.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_MindlinDeresiewitz.dict, yade.wrapper.GlBoundFunctor.dict, yade.wrapper.State.dict, yade.wrapper.ScGeom.dict, yade.wrapper.Peri3dController.dict, yade.wrapper.InterpolatingDirectedForceEngine.dict, yade.wrapper.ForceRecorder.dict, yade.wrapper.Ig2_GridConnection_PFacet_ScGeom.dict, yade.wrapper.PartialEngine.dict, yade.wrapper.ViscElCapPhys.dict, yade.wrapper.FlatGridCollider.dict, yade.wrapper.DeformableElement.dict, yade.wrapper.CapillaryTriaxialTest.dict, yade.wrapper.Ip2_LudingMat_LudingMat_LudingPhys.dict, yade.wrapper.LinIsoElastMat.dict, yade.wrapper.HarmonicRotationEngine.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom.dict, yade.wrapper.Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_Mindlin.dict, yade.wrapper.Ig2_Sphere_Polyhedra_ScGeom.dict, yade.wrapper.IGeomFunctor.dict, yade.wrapper.Ig2_Wall_Sphere_ScGeom.dict, yade.wrapper.DomainLimiter.dict, yade.wrapper.Gl1_ChainedCylinder.dict, yade.wrapper.If2_Lin4NodeTetra_LinIsoRayleighDampElast.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeom.dict, yade.wrapper.GlExtraDrawer.dict, yade.wrapper.HydroForceEngine.dict
writing... /home/hjz/yade2017/build/doc/sphinx/publications.rst:: WARNING: unusable reference target found: citing.html
/home/hjz/yade2017/build/doc/sphinx/publications.rst:: WARNING: unusable reference target found: citing.html
done
processing YadeManuals.tex... index-toctree_manuals introduction tutorial tutorial-introduction tutorial-hands-on tutorial-data-mining tutorial-geo tutorial-advanced tutorial-examples user prog installation github citing
resolving references...
writing... done
copying images... fig/qt-gui.png fig/yade-multi-summary.pdf fig/simple-scene-plot-4.pdf fig/simple-scene-plot-1.pdf fig/sweep-and-prune.pdf fig/yade-multi-gnuplot-merged.pdf fig/localstrain.png fig/predicate-difference.png fig/paraview-rendering-apply.png fig/spheres-contact-stiffness.pdf fig/yade-multi-gnuplot-single.pdf fig/funnel.pdf fig/paraview-glyph-icon.png fig/horse.png fig/cell-shear-aabb.pdf fig/yade-iter-loop.pdf fig/dispatch-loop.pdf fig/paraview-open-files.png fig/sphere-sphere.pdf fig/simple-scene-plot-3.pdf fig/hyperboloid.png fig/shear-2d.pdf fig/micro-domains.png fig/cell-flip.pdf fig/spheres-dofs.pdf fig/simple-scene-plot-2.pdf
copying TeX support files...
done
build succeeded, 17 warnings.
Running Sphinx v1.3.6
making output directory...
WARNING: the config value 'my_maketitle' is set to a string with non-ASCII characters; this can lead to Unicode errors occurring. Please use Unicode strings, e.g. u'Content'.
WARNING: extension 'youtube' has no setup() function; is it really a Sphinx extension module?
building [mo]: all of 0 po files
building [epub]: all source files
updating environment: 39 added, 0 changed, 0 removed
reading sources... [ 33%] introduction

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 321
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies[100]

IndexError: Body id out of range.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 327
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies.append(s)

IndexError: Body already has id 0 set; appending such body (for the second time) is not allowed.
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/introduction.rst at block ending on line 382
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.interactions[100,10111]

IndexError: No such interaction
<<<-------------------------------------------------------------------------

reading sources... [ 38%] prog

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 434
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 Sphere().name ## getClassName()

AttributeError: 'Sphere' object has no attribute 'name'
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/prog.rst at block ending on line 1466
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.forces.f(100)

IndexError: Body id out of range.
<<<-------------------------------------------------------------------------

reading sources... [ 58%] tutorial-hands-on

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 197
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 a[3] # error

IndexError: list index out of range
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 226
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 b[0]=4 # error

TypeError: 'tuple' object does not support item assignment
<<<-------------------------------------------------------------------------

>>>-------------------------------------------------------------------------
Exception in /home/hjz/yade2017/build/doc/sphinx/tutorial-hands-on.rst at block ending on line 383
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/__init__.py in <module>()
----> 1 O.bodies[1].shape.radius # radius of body #1 (will give error if not sphere, since only spheres have radius defined)

AttributeError: 'NoneType' object has no attribute 'shape'
<<<-------------------------------------------------------------------------

ERROR /home/hjz/yade2017/trunk/pkg/common/InsertionSortCollider.cpp:240 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.
reading sources... [100%] yade.ymport
/home/hjz/yade2017/build/doc/sphinx/index-toctree-manuals.rst:6: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/index-toctree-reference.rst:5: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/index-toctree-theory.rst:5: WARNING: toctree contains reference to nonexisting document u'fullPublications'
/home/hjz/yade2017/build/doc/sphinx/publications.rst:127: WARNING: Inline emphasis start-string without end-string.
/home/hjz/yade2017/build/doc/sphinx/publications.rst:429: WARNING: Duplicate explicit target name: "maurin2015".
/home/hjz/yade2017/build/doc/sphinx/publications.rst:429: WARNING: duplicate citation Maurin2015, other instance in /home/hjz/yade2017/build/doc/sphinx/publications.rst
/home/hjz/yade2017/build/doc/sphinx/yade.wrapper.rst:1: WARNING: malformed hyperlink target.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/hjz/yade2017/build/doc/sphinx/consulting.rst:: WARNING: document isn't included in any toctree
/home/hjz/yade2017/build/doc/sphinx/index-toctree-book.rst:: WARNING: document isn't included in any toctree
/home/hjz/yade2017/build/doc/sphinx/index-toctree_manuals.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the pngmath_latex setting
writing output... [100%] yade.ymport
/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:docstring of yade.utils.UnstructuredGrid:None: WARNING: more than one target found for cross-reference u'dict': yade.wrapper.Facet.dict, yade.wrapper.InsertionSortCollider.dict, yade.wrapper.ViscElCapMat.dict, yade.wrapper.LinearDragEngine.dict, yade.wrapper.Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.dict, yade.wrapper.CapillaryStressRecorder.dict, yade.wrapper.PFacet.dict, yade.wrapper.LawDispatcher.dict, yade.wrapper.FlowEngine_PeriodicInfo.dict, yade.wrapper.GridCoGridCoGeom.dict, yade.wrapper.CohesiveTriaxialTest.dict, yade.wrapper.NewtonIntegrator.dict, yade.wrapper.ViscElMat.dict, yade.wrapper.HydrodynamicsLawLBM.dict, yade.wrapper.CohFrictPhys.dict, yade.wrapper.Bo1_Polyhedra_Aabb.dict, yade.wrapper.IPhys.dict, yade.wrapper.GlobalStiffnessTimeStepper.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom6D.dict, yade.wrapper.Ip2_FrictMat_CpmMat_FrictPhys.dict, yade.wrapper.TetraVolumetricLaw.dict, yade.wrapper.KinemCNSEngine.dict, yade.wrapper.Gl1_GridConnection.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_HertzWithLinearShear.dict, yade.wrapper.GridNodeGeom6D.dict, yade.wrapper.CohesiveDeformableElementMaterial.dict, yade.wrapper.KinemSimpleShearBox.dict, yade.wrapper.Law2_L6Geom_FrictPhys_Linear.dict, yade.wrapper.L6Geom.dict, yade.wrapper.GlIPhysDispatcher.dict, yade.wrapper.CohFrictMat.dict, yade.wrapper.Bo1_PFacet_Aabb.dict, yade.wrapper.SumIntrForcesCb.dict, yade.wrapper.MindlinPhys.dict, yade.wrapper.Ip2_2xInelastCohFrictMat_InelastCohFrictPhys.dict, yade.wrapper.CpmStateUpdater.dict, yade.wrapper.Tetra.dict, yade.wrapper.Gl1_PolyhedraPhys.dict, yade.wrapper.ThreeDTriaxialEngine.dict, yade.wrapper.JCFpmState.dict, yade.wrapper.Bo1_Tetra_Aabb.dict, yade.wrapper.RungeKuttaCashKarp54Integrator.dict, yade.wrapper.Law2_ScGeom_MortarPhys_Lourenco.dict, yade.wrapper.Ig2_Sphere_Sphere_L3Geom.dict, yade.wrapper.Box.dict, yade.wrapper.PolyhedraSplitter.dict, yade.wrapper.LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.TimeStepper.dict, yade.wrapper.Gl1_Box.dict, yade.wrapper.ForceResetter.dict, yade.wrapper.Gl1_Tetra.dict, yade.wrapper.TriaxialTest.dict, yade.wrapper.PeriTriaxController.dict, yade.wrapper.PeriodicEngine.dict, yade.wrapper.InternalForceFunctor.dict, yade.wrapper.Gl1_PolyhedraGeom.dict, yade.wrapper.VTKRecorder.dict, yade.wrapper.Bo1_ChainedCylinder_Aabb.dict, yade.wrapper.Ip2_2xNormalInelasticMat_NormalInelasticityPhys.dict, yade.wrapper.Bound.dict, yade.wrapper.BubbleMat.dict, yade.wrapper.KinematicEngine.dict, yade.wrapper.RotationEngine.dict, yade.wrapper.ResetRandomPosition.dict, yade.wrapper.Law2_ScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.Law2_CylScGeom6D_CohFrictPhys_CohesionMoment.dict, yade.wrapper.FrictPhys.dict, yade.wrapper.Law2_ScGeom_BubblePhys_Bubble.dict, yade.wrapper.Gl1_CpmPhys.dict, yade.wrapper.GlobalEngine.dict, yade.wrapper.AxialGravityEngine.dict, yade.wrapper.NormPhys.dict, 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yade.wrapper.GlStateDispatcher.dict, yade.wrapper.Shape.dict, yade.wrapper.OpenGLRenderer.dict, yade.wrapper.Ip2_ElastMat_ElastMat_NormShearPhys.dict, yade.wrapper.ChCylGeom6D.dict, yade.wrapper.PolyhedraGeom.dict, yade.wrapper.Ig2_Facet_Polyhedra_PolyhedraGeom.dict, yade.wrapper.NormalInelasticityPhys.dict, yade.wrapper.Ig2_Tetra_Tetra_TTetraSimpleGeom.dict, yade.wrapper.HelixEngine.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom.dict, yade.wrapper.CapillaryPhys.dict, yade.wrapper.LawTester.dict, yade.wrapper.Ig2_Sphere_Sphere_ScGeom.dict, yade.wrapper.ViscoFrictPhys.dict, yade.wrapper.Gl1_NormPhys.dict, yade.wrapper.Clump.dict, yade.wrapper.IPhysFunctor.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom.dict, yade.wrapper.Cylinder.dict, yade.wrapper.Ig2_GridNode_GridNode_GridNodeGeom6D.dict, yade.wrapper.SnapshotEngine.dict, yade.wrapper.TorqueRecorder.dict, yade.wrapper.ParallelEngine.dict, yade.wrapper.InelastCohFrictPhys.dict, yade.wrapper.Bo1_Box_Aabb.dict, 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yade.wrapper.Bo1_Facet_Aabb.dict, yade.wrapper.GravityEngine.dict, yade.wrapper.Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys.dict, yade.wrapper.KinemCTDEngine.dict, yade.wrapper.BubblePhys.dict, yade.wrapper.Ip2_FrictMat_FrictMat_MindlinPhys.dict, yade.wrapper.BoundDispatcher.dict, yade.wrapper.InterpolatingHelixEngine.dict, yade.wrapper.Law2_ScGeom_FrictPhys_CundallStrack.dict, yade.wrapper.Bo1_GridConnection_Aabb.dict, yade.wrapper.Ip2_BubbleMat_BubbleMat_BubblePhys.dict, yade.wrapper.BoundFunctor.dict, yade.wrapper.Bo1_Cylinder_Aabb.dict, yade.wrapper.Law2_TTetraSimpleGeom_NormPhys_Simple.dict, yade.wrapper.MindlinCapillaryPhys.dict, yade.wrapper.Gl1_Polyhedra.dict, yade.wrapper.IPhysDispatcher.dict, yade.wrapper.Ip2_FrictMat_FrictMat_FrictPhys.dict, yade.wrapper.If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.dict, yade.wrapper.NormalInelasticMat.dict, yade.wrapper.FacetTopologyAnalyzer.dict, yade.wrapper.GlIPhysFunctor.dict, 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yade.wrapper.Ig2_Sphere_Sphere_ScGeom6D.dict, yade.wrapper.CentralGravityEngine.dict, yade.wrapper.UniaxialStrainer.dict, yade.wrapper.FrictMat.dict, yade.wrapper.CylScGeom.dict, yade.wrapper.GlExtra_LawTester.dict, yade.wrapper.Law2_ScGeom_WirePhys_WirePM.dict, yade.wrapper.InternalForceDispatcher.dict, yade.wrapper.Ig2_Sphere_Sphere_L6Geom.dict, yade.wrapper.Law2_PolyhedraGeom_PolyhedraPhys_Volumetric.dict, yade.wrapper.GridNode.dict, yade.wrapper.FileGenerator.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom6D.dict, yade.wrapper.Ig2_PFacet_PFacet_ScGeom.dict, yade.wrapper.CpmPhys.dict, yade.wrapper.Ig2_Facet_Sphere_L3Geom.dict, yade.wrapper.Ip2_FrictMat_FrictMat_CapillaryPhys.dict, yade.wrapper.ViscElPhys.dict, yade.wrapper.EnergyTracker.dict, yade.wrapper.Ig2_GridConnection_GridConnection_GridCoGridCoGeom.dict, yade.wrapper.Aabb.dict, yade.wrapper.FieldApplier.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_MindlinDeresiewitz.dict, yade.wrapper.GlBoundFunctor.dict, yade.wrapper.State.dict, yade.wrapper.ScGeom.dict, yade.wrapper.Peri3dController.dict, yade.wrapper.InterpolatingDirectedForceEngine.dict, yade.wrapper.ForceRecorder.dict, yade.wrapper.Ig2_GridConnection_PFacet_ScGeom.dict, yade.wrapper.PartialEngine.dict, yade.wrapper.ViscElCapPhys.dict, yade.wrapper.FlatGridCollider.dict, yade.wrapper.DeformableElement.dict, yade.wrapper.CapillaryTriaxialTest.dict, yade.wrapper.Ip2_LudingMat_LudingMat_LudingPhys.dict, yade.wrapper.LinIsoElastMat.dict, yade.wrapper.HarmonicRotationEngine.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom.dict, yade.wrapper.Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_Mindlin.dict, yade.wrapper.Ig2_Sphere_Polyhedra_ScGeom.dict, yade.wrapper.IGeomFunctor.dict, yade.wrapper.Ig2_Wall_Sphere_ScGeom.dict, yade.wrapper.DomainLimiter.dict, yade.wrapper.Gl1_ChainedCylinder.dict, yade.wrapper.If2_Lin4NodeTetra_LinIsoRayleighDampElast.dict, 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/home/hjz/yade2017/install/lib/x86_64-linux-gnu/yade-2017.01a/py/yade/utils.py:docstring of yade.utils.UnstructuredGrid:None: WARNING: more than one target found for cross-reference u'dict': yade.wrapper.Facet.dict, yade.wrapper.InsertionSortCollider.dict, yade.wrapper.ViscElCapMat.dict, yade.wrapper.LinearDragEngine.dict, yade.wrapper.Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.dict, yade.wrapper.CapillaryStressRecorder.dict, yade.wrapper.PFacet.dict, yade.wrapper.LawDispatcher.dict, yade.wrapper.FlowEngine_PeriodicInfo.dict, yade.wrapper.GridCoGridCoGeom.dict, yade.wrapper.CohesiveTriaxialTest.dict, yade.wrapper.NewtonIntegrator.dict, yade.wrapper.ViscElMat.dict, yade.wrapper.HydrodynamicsLawLBM.dict, yade.wrapper.CohFrictPhys.dict, yade.wrapper.Bo1_Polyhedra_Aabb.dict, yade.wrapper.IPhys.dict, yade.wrapper.GlobalStiffnessTimeStepper.dict, yade.wrapper.Ig2_Box_Sphere_ScGeom6D.dict, yade.wrapper.Ip2_FrictMat_CpmMat_FrictPhys.dict, yade.wrapper.TetraVolumetricLaw.dict, 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yade.wrapper.Ig2_Sphere_Sphere_ScGeom6D.dict, yade.wrapper.CentralGravityEngine.dict, yade.wrapper.UniaxialStrainer.dict, yade.wrapper.FrictMat.dict, yade.wrapper.CylScGeom.dict, yade.wrapper.GlExtra_LawTester.dict, yade.wrapper.Law2_ScGeom_WirePhys_WirePM.dict, yade.wrapper.InternalForceDispatcher.dict, yade.wrapper.Ig2_Sphere_Sphere_L6Geom.dict, yade.wrapper.Law2_PolyhedraGeom_PolyhedraPhys_Volumetric.dict, yade.wrapper.GridNode.dict, yade.wrapper.FileGenerator.dict, yade.wrapper.Ig2_Sphere_ChainedCylinder_CylScGeom6D.dict, yade.wrapper.Ig2_PFacet_PFacet_ScGeom.dict, yade.wrapper.CpmPhys.dict, yade.wrapper.Ig2_Facet_Sphere_L3Geom.dict, yade.wrapper.Ip2_FrictMat_FrictMat_CapillaryPhys.dict, yade.wrapper.ViscElPhys.dict, yade.wrapper.EnergyTracker.dict, yade.wrapper.Ig2_GridConnection_GridConnection_GridCoGridCoGeom.dict, yade.wrapper.Aabb.dict, yade.wrapper.FieldApplier.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_MindlinDeresiewitz.dict, yade.wrapper.GlBoundFunctor.dict, yade.wrapper.State.dict, yade.wrapper.ScGeom.dict, yade.wrapper.Peri3dController.dict, yade.wrapper.InterpolatingDirectedForceEngine.dict, yade.wrapper.ForceRecorder.dict, yade.wrapper.Ig2_GridConnection_PFacet_ScGeom.dict, yade.wrapper.PartialEngine.dict, yade.wrapper.ViscElCapPhys.dict, yade.wrapper.FlatGridCollider.dict, yade.wrapper.DeformableElement.dict, yade.wrapper.CapillaryTriaxialTest.dict, yade.wrapper.Ip2_LudingMat_LudingMat_LudingPhys.dict, yade.wrapper.LinIsoElastMat.dict, yade.wrapper.HarmonicRotationEngine.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom.dict, yade.wrapper.Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity.dict, yade.wrapper.Law2_ScGeom_MindlinPhys_Mindlin.dict, yade.wrapper.Ig2_Sphere_Polyhedra_ScGeom.dict, yade.wrapper.IGeomFunctor.dict, yade.wrapper.Ig2_Wall_Sphere_ScGeom.dict, yade.wrapper.DomainLimiter.dict, yade.wrapper.Gl1_ChainedCylinder.dict, yade.wrapper.If2_Lin4NodeTetra_LinIsoRayleighDampElast.dict, yade.wrapper.Ig2_Polyhedra_Polyhedra_PolyhedraGeom.dict, yade.wrapper.GlExtraDrawer.dict, yade.wrapper.HydroForceEngine.dict
docstring of yade.wrapper.Ip2_JCFpmMat_JCFpmMat_JCFpmPhys:1: WARNING: citation not found: Duriez2016
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Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Anton Gladky
Solved:
Last query:
Last reply:
Revision history for this message
Jan Stránský (honzik) said : 		#1

Hello,
have you read yade/doc/sphinx/README ? I create documentation with
command(s)

cd /path/to/yade/doc/sphinx
PYTHONPATH=. yade-trunk -x yadeSphinx.py

cheers
Jan

Revision history for this message
hjz (1341132388-4) said : 		#3

Hi Jan,
      Maybe a firewall happened to me. When I executed the code: sudo apt-add-repository ppa:yade-users/external & sudo apt-get update, a warning came out: the repository “http://ppa.launchpad.net/yade-users/external/ubuntu xenial Release” does not have a Release file.
      So, if I don't install the doc, it wouldn't influence me in using the YADE, would it?
Best wishes
hjz

Revision history for this message
Best Anton Gladky (gladky-anton) said : 		#4

You do not need to install Sphinx from external repository.
That requirement in README is obsolete and only for
very old distributions.

Regards

Anton

Revision history for this message
hjz (1341132388-4) said : 		#5

Thanks Anton Gladky, that solved my question.

Revision history for this message
Bruno Chareyre (bruno-chareyre) said : 		#6

Does #4 really answer the question??
I would think the real problem was this:
/bin/sh: 1: xelatex: not found

You need xelatex compiler to generate the pdf.

Bruno

p.s. @Jan, Anton, I found that the old "PYTHONPATH=. yade-trunk -x yadeSphinx.py" was not working some time ago, and that only "make doc" was doing the job correctly, but it depends on many things IIRC (for instance executing the command in trunk/doc or in build/doc is not necessarily the same).

Revision history for this message
Anton Gladky (gladky-anton) said : 		#7

Well, it was planned to replace the documentation generation by a a simple "make doc". I do not remember why, but it did not worked well everywhere. That is why we still have "yade yadeSphinx...." magic in debian builds.

"make doc" is supposed to be executed __only__ in build directory, and it must not be the same as a source one.

Revision history for this message
hjz (1341132388-4) said : 		#8

Well, when I saw a new folder-sphinx was generated in the doc/sphinx folder, I thought simply that I was successful. There was not a pdf file generated indeed. I would try again with the xelatex compiler.