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1	·7e261d88a10e9db6aa14a52df113e673·12976288·debug·optional·libyade-dbgsym_2025.2.0-1_arm64.deb	1	·7e261d88a10e9db6aa14a52df113e673·12976288·debug·optional·libyade-dbgsym_2025.2.0-1_arm64.deb
2	·3956f899c679dd476788571e6386e2ad·48537916·science·optional·libyade_2025.2.0-1_arm64.deb	2	·3956f899c679dd476788571e6386e2ad·48537916·science·optional·libyade_2025.2.0-1_arm64.deb
3	·5c32c170b683de8d868031059994b357·303436·python·optional·python3-yade_2025.2.0-1_arm64.deb	3	·5c32c170b683de8d868031059994b357·303436·python·optional·python3-yade_2025.2.0-1_arm64.deb
4	·398c158ac9ca1e05f10~~b3b~~5~~4cf0~~d~~3c52~~·18~~803636~~·doc·optional·yade-doc_2025.2.0-1_all.deb	4	·90a1bcb4130f1c698028d95b693dcb97·18795988·doc·optional·yade-doc_2025.2.0-1_all.deb
5	·1cdfe027265c38044765dda2c4525792·2235220·science·optional·yade_2025.2.0-1_arm64.deb	5	·1cdfe027265c38044765dda2c4525792·2235220·science·optional·yade_2025.2.0-1_arm64.deb


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1	-rw-r--r--···0········0········0········4·2025-02-10·05:43:53.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2025-02-10·05:43:53.000000·debian-binary
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3	-rw-r--r--···0········0········0·187~~94420~~·2025-02-10·05:43:53.000000·data.tar.xz	3	-rw-r--r--···0········0········0·18786764·2025-02-10·05:43:53.000000·data.tar.xz


Offset 1, 13 lines modified		Offset 1, 13 lines modified
1	Package:·yade-doc	1	Package:·yade-doc
2	Source:·yade	2	Source:·yade
3	Version:·2025.2.0-1	3	Version:·2025.2.0-1
4	Architecture:·all	4	Architecture:·all
5	Maintainer:·Debian·Science·Maintainers·<debian-science-maintainers@lists.alioth.debian.org>	5	Maintainer:·Debian·Science·Maintainers·<debian-science-maintainers@lists.alioth.debian.org>
6	Installed-Size:·42220	6	Installed-Size:·42212
7	Depends:·libjs-jquery·(>=·3.6.0),·libjs-sphinxdoc·(>=·8.1),·libjs-mathjax	7	Depends:·libjs-jquery·(>=·3.6.0),·libjs-sphinxdoc·(>=·8.1),·libjs-mathjax
8	Recommends:·yade	8	Recommends:·yade
9	Section:·doc	9	Section:·doc
10	Priority:·optional	10	Priority:·optional
11	Multi-Arch:·foreign	11	Multi-Arch:·foreign
12	Homepage:·https://yade-dem.org/doc/	12	Homepage:·https://yade-dem.org/doc/
13	Description:·Platform·for·discrete·element·modeling.·Documentation	13	Description:·Platform·for·discrete·element·modeling.·Documentation


Offset 1, 10 lines modified		Offset 1, 10 lines modified
1	Yade·Documentation·(3rd·ed.)	1	Yade·Documentation·(3rd·ed.)

2	3rd·Edition·based·on·Yade·version·2025.2.0,·July·27,·2025	2	3rd·Edition·based·on·Yade·version·2025.2.0,·August·31,·2026

3	\xcAuthors	3	\xcAuthors
4	•·Václav·Šmilauer·Freelance·consultant·(http://woodem.eu)	4	•·Václav·Šmilauer·Freelance·consultant·(http://woodem.eu)
5	•·Vasileios·Angelidakis·Newcastle·University,·UK	5	•·Vasileios·Angelidakis·Newcastle·University,·UK
6	•·Emanuele·Catalano·Univ.·Grenoble·Alpes,·3SR·lab.	6	•·Emanuele·Catalano·Univ.·Grenoble·Alpes,·3SR·lab.
7	•·Robert·Caulk·Univ.·Grenoble·Alpes,·3SR·lab.	7	•·Robert·Caulk·Univ.·Grenoble·Alpes,·3SR·lab.
8	•·Bruno·Chareyre·Univ.·Grenoble·Alpes,·3SR·lab.	8	•·Bruno·Chareyre·Univ.·Grenoble·Alpes,·3SR·lab.
Offset 516, 28 lines modified		Offset 516, 28 lines modified
516	O.pause();·note·that·O.run()·returns·control·to·Python·and·the·simulation·runs·in·background;·if	516	O.pause();·note·that·O.run()·returns·control·to·Python·and·the·simulation·runs·in·background;·if
517	you·want·to·wait·for·it·to·finish,·use·O.wait().·Fixed·number·of·steps·can·be·run·with·O.run(1000),	517	you·want·to·wait·for·it·to·finish,·use·O.wait().·Fixed·number·of·steps·can·be·run·with·O.run(1000),
518	O.run(1000,True)·will·run·and·wait.·To·stop·at·absolute·step·number,·O.stopAtIter·can·be·set·and	518	O.run(1000,True)·will·run·and·wait.·To·stop·at·absolute·step·number,·O.stopAtIter·can·be·set·and
519	O.run()·called·normally.	519	O.run()·called·normally.
520	Yade·[12]:·O.run()	520	Yade·[12]:·O.run()
521	Yade·[13]:·O.pause()	521	Yade·[13]:·O.pause()
522	Yade·[14]:·O.iter	522	Yade·[14]:·O.iter
523	Out[14]:·~~548~~	523	Out[14]:·600
524	Yade·[15]:·O.run(100000,True)	524	Yade·[15]:·O.run(100000,True)
525	Yade·[16]:·O.iter	525	Yade·[16]:·O.iter
526	(continues·on·next·page)	526	(continues·on·next·page)

527	4	527	4

528	Chapter·1.·Guided·tour	528	Chapter·1.·Guided·tour

529	\xcYade·Documentation,·Release·3rd·ed.	529	\xcYade·Documentation,·Release·3rd·ed.

530	(continued·from·previous·page)	530	(continued·from·previous·page)

531	Out[16]:·100~~548~~	531	Out[16]:·100600
532	Yade·[17]:·O.stopAtIter=500000	532	Yade·[17]:·O.stopAtIter=500000
533	Yade·[18]:·O.run()	533	Yade·[18]:·O.run()
534	Yade·[19]:·O.wait()	534	Yade·[19]:·O.wait()
535	Yade·[20]:·O.iter	535	Yade·[20]:·O.iter
536	Out[20]:·500000	536	Out[20]:·500000
537	Saving·and·loading	537	Saving·and·loading
538	Simulation·can·be·saved·at·any·point·to·a·binary·file·(optionaly·compressed·if·the·filename·has·extensions	538	Simulation·can·be·saved·at·any·point·to·a·binary·file·(optionaly·compressed·if·the·filename·has·extensions
Offset 605, 15 lines modified		Offset 605, 15 lines modified
605	To·assure·flexibility·of·software·design,·yade·makes·clear·distinction·of·2·families·of·classes:·data·components·and·functional·components.·The·former·only·store·data·without·providing·functionality,·while	605	To·assure·flexibility·of·software·design,·yade·makes·clear·distinction·of·2·families·of·classes:·data·components·and·functional·components.·The·former·only·store·data·without·providing·functionality,·while
606	the·latter·define·functions·operating·on·the·data.·In·programming,·this·is·known·as·visitor·pattern·(as	606	the·latter·define·functions·operating·on·the·data.·In·programming,·this·is·known·as·visitor·pattern·(as
607	functional·components·“visit”·the·data,·without·being·bound·to·them·explicitly).	607	functional·components·“visit”·the·data,·without·being·bound·to·them·explicitly).
608	Entire·simulation,·i.e.·both·data·and·functions,·are·stored·in·a·single·Scene·object.·It·is·accessible	608	Entire·simulation,·i.e.·both·data·and·functions,·are·stored·in·a·single·Scene·object.·It·is·accessible
609	through·the·Omega·class·in·python·(a·singleton),·which·is·by·default·stored·in·the·O·global·variable:	609	through·the·Omega·class·in·python·(a·singleton),·which·is·by·default·stored·in·the·O·global·variable:
610	Yade·[28]:·O.bodies	610	Yade·[28]:·O.bodies
611	#·some·data·components	611	#·some·data·components
612	Out[28]:·<yade.wrapper.BodyContainer·at·0xffff686149e0>	612	Out[28]:·<yade.wrapper.BodyContainer·at·0xffff768e4970>
613	Yade·[29]:·len(O.bodies)	613	Yade·[29]:·len(O.bodies)
614	Out[29]:·0	614	Out[29]:·0

615	#·there·are·no·bodies·as·of·yet	615	#·there·are·no·bodies·as·of·yet

616	Yade·[30]:·O.engines	616	Yade·[30]:·O.engines
617	Out[30]:·[]	617	Out[30]:·[]
Offset 667, 17 lines modified		Offset 667, 17 lines modified

667	\xcYade·Documentation,·Release·3rd·ed.	667	\xcYade·Documentation,·Release·3rd·ed.

668	(continued·from·previous·page)	668	(continued·from·previous·page)

669	Yade·[32]:·s.shape,·s.state,·s.mat,·s.bound	669	Yade·[32]:·s.shape,·s.state,·s.mat,·s.bound
670	Out[32]:	670	Out[32]:
671	(<Sphere·instance·at·0x~~1efe938~~0>,	671	(<Sphere·instance·at·0x37db41a0>,
672	<State·instance·at·0x~~1ee33fc~~0>,	672	<State·instance·at·0x37d8e710>,
673	<FrictMat·instance·at·0x~~1ef~~7~~403~~0>,	673	<FrictMat·instance·at·0x37d7e620>,
674	None)	674	None)
675	Yade·[33]:·s.state.pos	675	Yade·[33]:·s.state.pos
676	Out[33]:·Vector3(0,0,0)	676	Out[33]:·Vector3(0,0,0)
677	Yade·[34]:·s.shape.radius	677	Yade·[34]:·s.shape.radius
678	Out[34]:·1.0	678	Out[34]:·1.0
679	We·see·that·a·sphere·with·material·of·type·FrictMat·(default,·unless·you·provide·another·Material)·and	679	We·see·that·a·sphere·with·material·of·type·FrictMat·(default,·unless·you·provide·another·Material)·and
680	bounding·volume·of·type·Aabb·(axis-aligned·bounding·box)·was·created.·Its·position·is·at·the·origin·and	680	bounding·volume·of·type·Aabb·(axis-aligned·bounding·box)·was·created.·Its·position·is·at·the·origin·and
Offset 745, 35 lines modified		Offset 745, 35 lines modified
745	representing·non-geometrical·features·of·the·interaction;·some·are·computed·from·Materials·of·the	745	representing·non-geometrical·features·of·the·interaction;·some·are·computed·from·Materials·of·the
746	particles·in·contact·using·some·averaging·algorithm·(such·as·contact·stiffness·from·Young’s·moduli	746	particles·in·contact·using·some·averaging·algorithm·(such·as·contact·stiffness·from·Young’s·moduli
747	of·particles),·others·might·be·internal·variables·like·damage.	747	of·particles),·others·might·be·internal·variables·like·damage.

748	Fig.·2:·Examples·of·concrete·classes·that·might·be·used·to·describe·an·Interaction:·IGeom,·GenericSpheresContact,·PolyhedraGeom,·CylScGeom,·IPhys,·NormPhys,·NormShearPhys,·FrictPhys.	748	Fig.·2:·Examples·of·concrete·classes·that·might·be·used·to·describe·an·Interaction:·IGeom,·GenericSpheresContact,·PolyhedraGeom,·CylScGeom,·IPhys,·NormPhys,·NormShearPhys,·FrictPhys.
749	Suppose·now·interactions·have·been·already·created.·We·can·access·them·by·the·id·pair:	749	Suppose·now·interactions·have·been·already·created.·We·can·access·them·by·the·id·pair:
750	Yade·[41]:·O.interactions[0,1]	750	Yade·[41]:·O.interactions[0,1]
751	Out[41]:·<Interaction·instance·at·0x~~1ef79ed~~0>	751	Out[41]:·<Interaction·instance·at·0x37d44f10>
752	Yade·[42]:·O.interactions[1,0]	752	Yade·[42]:·O.interactions[1,0]
753	#·order·of·ids·is·not·important	753	#·order·of·ids·is·not·important
754	Out[42]:·<Interaction·instance·at·0x~~1ef79ed~~0>	754	Out[42]:·<Interaction·instance·at·0x37d44f10>
755	Yade·[43]:·i=O.interactions[0,1]	755	Yade·[43]:·i=O.interactions[0,1]
756	(continues·on·next·page)	756	(continues·on·next·page)

757	10	757	10

758	Chapter·1.·Guided·tour	758	Chapter·1.·Guided·tour

759	\xcYade·Documentation,·Release·3rd·ed.	759	\xcYade·Documentation,·Release·3rd·ed.

760	(continued·from·previous·page)	760	(continued·from·previous·page)

761	Yade·[44]:·i.id1,i.id2	761	Yade·[44]:·i.id1,i.id2
762	Out[44]:·(0,·1)	762	Out[44]:·(0,·1)
763	Yade·[45]:·i.geom	763	Yade·[45]:·i.geom
764	Out[45]:·<ScGeom·instance·at·0x~~1ee8766~~0>	764	Out[45]:·<ScGeom·instance·at·0x37da6ed0>
765	Yade·[46]:·i.phys	765	Yade·[46]:·i.phys
766	Out[46]:·<FrictPhys·instance·at·0x~~1ef7dbf~~0>	766	Out[46]:·<FrictPhys·instance·at·0x37e82540>
767	Yade·[47]:·O.interactions[100,10111]	767	Yade·[47]:·O.interactions[100,10111]
768	#·asking·for·non·existing·interaction·throws␣	768	#·asking·for·non·existing·interaction·throws␣
769	,→exception	769	,→exception
770	[0;31m---------------------------------------------------------------------------[0m	770	[0;31m---------------------------------------------------------------------------[0m
771	[0;31mIndexError[0m	771	[0;31mIndexError[0m
772	Traceback·(most·recent·call·last)	772	Traceback·(most·recent·call·last)
773	Cell·[0;32mIn[47],·line·1[0m	773	Cell·[0;32mIn[47],·line·1[0m
Offset 1400, 15 lines modified		Offset 1400, 15 lines modified
1400	,→with·radius=1	1400	,→with·radius=1

1401	#·create·sphere·particle·centered·at·(0,0,0)␣	1401	#·create·sphere·particle·centered·at·(0,0,0)␣

1402	Yade·[44]:·s.shape	1402	Yade·[44]:·s.shape
1403	#·s.shape·describes·the·geometry·of·the␣	1403	#·s.shape·describes·the·geometry·of·the␣
1404	,→particle	1404	,→particle
1405	Out[44]:·<Sphere·instance·at·0x~~1f13f72~~0>	1405	Out[44]:·<Sphere·instance·at·0x384ac0b0>
1406	Yade·[45]:·s.shape.radius	1406	Yade·[45]:·s.shape.radius
1407	Out[45]:·1.0	1407	Out[45]:·1.0

1408	#·we·already·know·the·Sphere·class	1408	#·we·already·know·the·Sphere·class

1409	Yade·[46]:·s.state.mass,·s.state.inertia·#·inertia·is·computed·from·density·and␣	1409	Yade·[46]:·s.state.mass,·s.state.inertia·#·inertia·is·computed·from·density·and␣
1410	,→geometry	1410	,→geometry
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30	usr/share/doc/yade/html/_images/dispatch-loop.png	30	usr/share/doc/yade/html/_images/dispatch-loop.png
31	usr/share/doc/yade/html/_images/funnel.png	31	usr/share/doc/yade/html/_images/funnel.png
32	usr/share/doc/yade/html/_images/gnuplot.png	32	usr/share/doc/yade/html/_images/gnuplot.png
33	usr/share/doc/yade/html/_images/graphviz-026e1bdf412147766472ddfdaf48b32402babcac.png	33	usr/share/doc/yade/html/_images/graphviz-026e1bdf412147766472ddfdaf48b32402babcac.png
34	usr/share/doc/yade/html/_images/graphviz-026e1bdf412147766472ddfdaf48b32402babcac.png.map	34	usr/share/doc/yade/html/_images/graphviz-026e1bdf412147766472ddfdaf48b32402babcac.png.map
35	usr/share/doc/yade/html/_images/graphviz-0aefe59e00f45abaf0ae5974b5afcf3876f5e1ce.png	35	usr/share/doc/yade/html/_images/graphviz-0aefe59e00f45abaf0ae5974b5afcf3876f5e1ce.png
36	usr/share/doc/yade/html/_images/graphviz-0aefe59e00f45abaf0ae5974b5afcf3876f5e1ce.png.map	36	usr/share/doc/yade/html/_images/graphviz-0aefe59e00f45abaf0ae5974b5afcf3876f5e1ce.png.map
37	usr/share/doc/yade/html/_images/graphviz-175cf273b2a9969f4de1ce25e1f6bdc24143212b.png
38	usr/share/doc/yade/html/_images/graphviz-~~175cf273~~b~~2a996~~9~~f4de~~1~~ce25e1~~f6b~~dc24143212b~~.png~~.map~~	37	usr/share/doc/yade/html/_images/graphviz-0d745910bd20009e96213af0b0fbbeeccd2eee78.png
		38	usr/share/doc/yade/html/_images/graphviz-0d745910bd20009e96213af0b0fbbeeccd2eee78.png.map
39	usr/share/doc/yade/html/_images/graphviz-17f9812096113ae486215e7db30e452a557e728d.png	39	usr/share/doc/yade/html/_images/graphviz-17f9812096113ae486215e7db30e452a557e728d.png
40	usr/share/doc/yade/html/_images/graphviz-17f9812096113ae486215e7db30e452a557e728d.png.map	40	usr/share/doc/yade/html/_images/graphviz-17f9812096113ae486215e7db30e452a557e728d.png.map
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Offset 34, 50 lines modified		Offset 34, 50 lines modified
34	..·graphviz::	34	..·graphviz::
35	» :caption:·Inheritance·graph·of·Shape.	35	» :caption:·Inheritance·graph·of·Shape.

36	» digraph·Shape·{	36	» digraph·Shape·{
37	» » rankdir=RL;	37	» » rankdir=RL;
38	» » margin="0.2,0.05";	38	» » margin="0.2,0.05";
39	» » "Shape"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Shape"];	39	» » "Shape"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Shape"];
40	» » "~~Clump~~"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.~~Clump~~"];	40	» » "Sphere"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
41	» » "~~Clump~~"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	41	» » "Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
42	» » "LevelSet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];
43	» » "LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
44	» » "Node"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];	42	» » "Node"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];
45	» » "Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	43	» » "Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
46	» » "DeformableElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];	44	» » "DeformableElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];
47	» » "DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	45	» » "DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		46	» » "PFacet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
		47	» » "PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		48	» » "Wall"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];
		49	» » "Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		50	» » "Facet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
		51	» » "Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
48	» » "GridNode"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];	52	» » "GridNode"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];
49	» » "GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	53	» » "GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
50	» » "Cylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
51	» » "Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
52	» » "DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];
53	» » "DeformableCohesiveElement"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
54	» » "PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
55	» » "PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
56	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
57	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·->·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
58	» » "ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];	54	» » "ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];
59	» » "ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth(0.5)"];	55	» » "ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth(0.5)"];
60	» » "PFacet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
61	» » "PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
62	» » "Sphere"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
63	» » "Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
64	» » "Tetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];	56	» » "Tetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];
65	» » "Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	57	» » "Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
66	» » "Box"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];
67	» » "Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
68	» » "Facet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
69	» » "Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
70	» » "Wall"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];
71	» » "Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
72	» » "GridConnection"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridConnection"];	58	» » "GridConnection"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridConnection"];
73	» » "GridConnection"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	59	» » "GridConnection"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		60	» » "Box"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];
		61	» » "Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		62	» » "Cylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
		63	» » "Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		64	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
		65	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·->·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
74	» » "Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];	66	» » "Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];
75	» » "Lin4NodeTetra"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];	67	» » "Lin4NodeTetra"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		68	» » "LevelSet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];
		69	» » "LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		70	» » "DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];
		71	» » "DeformableCohesiveElement"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		72	» » "Clump"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Clump"];
		73	» » "Clump"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		74	» » "PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
		75	» » "PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
76	» }	76	» }

77	..·autoclass::·Shape	77	..·autoclass::·Shape
78	» :members:	78	» :members:
79	» :undoc-members:	79	» :undoc-members:
80	» :inherited-members:	80	» :inherited-members:

Offset 183, 22 lines modified		Offset 183, 22 lines modified

183	» digraph·State·{	183	» digraph·State·{
184	» » rankdir=RL;	184	» » rankdir=RL;
185	» » margin="0.2,0.05";	185	» » margin="0.2,0.05";
186	» » "State"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.State"];	186	» » "State"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.State"];
187	» » "ChainedState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedState"];	187	» » "ChainedState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedState"];
188	» » "ChainedState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	188	» » "ChainedState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
189	» » "WireState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireState"];
190	» » "WireState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
191	» » "JCFpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.JCFpmState"];
192	» » "JCFpmState"·->·"ThermalState"·[arrowsize=0.5,style="setlinewidth(0.5)"];
193	» » "CpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CpmState"];	189	» » "CpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CpmState"];
194	» » "CpmState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	190	» » "CpmState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		191	» » "WireState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireState"];
		192	» » "WireState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
195	» » "ThermalState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ThermalState"];	193	» » "ThermalState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ThermalState"];
196	» » "ThermalState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	194	» » "ThermalState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		195	» » "JCFpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.JCFpmState"];
		196	» » "JCFpmState"·->·"ThermalState"·[arrowsize=0.5,style="setlinewidth(0.5)"];
197	» }	197	» }

198	..·autoclass::·State	198	..·autoclass::·State
199	» :members:	199	» :members:
200	» :undoc-members:	200	» :undoc-members:
201	» :inherited-members:	201	» :inherited-members:

Offset 237, 54 lines modified		Offset 237, 54 lines modified
237	..·graphviz::	237	..·graphviz::
238	» :caption:·Inheritance·graph·of·Material.	238	» :caption:·Inheritance·graph·of·Material.

239	» digraph·Material·{	239	» digraph·Material·{
240	» » rankdir=RL;	240	» » rankdir=RL;
241	» » margin="0.2,0.05";	241	» » margin="0.2,0.05";
242	» » "Material"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Material"];	242	» » "Material"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Material"];
		243	» » "ViscElCapMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ViscElCapMat"];
		244	» » "ViscElCapMat"·->·"ViscElMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		245	» » "MortarMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.MortarMat"];
		246	» » "MortarMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		247	» » "LinIsoElastMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LinIsoElastMat"];
		248	» » "LinIsoElastMat"·->·"DeformableElementMaterial"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		249	» » "LinCohesiveElasticMaterial"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LinCohesiveElasticMaterial"];
		250	» » "LinCohesiveElasticMaterial"·->·"CohesiveDeformableElementMaterial"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		251	» » "FrictMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictMat"];
		252	» » "FrictMat"·->·"ElastMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		253	» » "LudingMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LudingMat"];
		254	» » "LudingMat"·->·"Material"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		255	» » "BubbleMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.BubbleMat"];
		256	» » "BubbleMat"·->·"Material"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		257	» » "LinCohesiveStiffPropDampElastMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LinCohesiveStiffPropDampElastMat"];
		258	» » "LinCohesiveStiffPropDampElastMat"·->·"LinCohesiveElasticMaterial"·[arrowsize=0.5,style="setlinewidth(0.5)"];
243	» » "FrictViscoMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictViscoMat"];	259	» » "FrictViscoMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictViscoMat"];
244	» » "FrictViscoMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];	260	» » "FrictViscoMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
245	» » "CpmMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CpmMat"];	261	» » "CohFrictMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CohFrictMat"];
246	» » "CpmMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];	262	» » "CohFrictMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
247	» » "WireMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireMat"];
248	» » "WireMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
Max diff block lines reached; 121874/133095 bytes (91.57%) of diff not shown.


Offset 242, 20 lines modified		Offset 242, 20 lines modified
242	(1000,True)·will·run·and·wait.·To·stop·at·absolute·step·number,·O.stopAtIter	242	(1000,True)·will·run·and·wait.·To·stop·at·absolute·step·number,·O.stopAtIter
243	can·be·set·and·O.run()·called·normally.	243	can·be·set·and·O.run()·called·normally.
244	Yade·[12]:·O.run()	244	Yade·[12]:·O.run()

245	Yade·[13]:·O.pause()	245	Yade·[13]:·O.pause()

246	Yade·[14]:·O.iter	246	Yade·[14]:·O.iter
247	Out[14]:·~~558~~	247	Out[14]:·723

248	Yade·[15]:·O.run(100000,True)	248	Yade·[15]:·O.run(100000,True)

249	Yade·[16]:·O.iter	249	Yade·[16]:·O.iter
250	Out[16]:·100~~558~~	250	Out[16]:·100723

251	Yade·[17]:·O.stopAtIter=500000	251	Yade·[17]:·O.stopAtIter=500000

252	Yade·[18]:·O.run()	252	Yade·[18]:·O.run()

253	Yade·[19]:·O.wait()	253	Yade·[19]:·O.wait()

Offset 334, 15 lines modified		Offset 334, 15 lines modified
334	operating·on·the·data.·In·programming,·this·is·known·as·v\x8vi\x8is\x8si\x8it\x8to\x8or\x8r·pattern·(as	334	operating·on·the·data.·In·programming,·this·is·known·as·v\x8vi\x8is\x8si\x8it\x8to\x8or\x8r·pattern·(as
335	functional·components·“visit”·the·data,·without·being·bound·to·them	335	functional·components·“visit”·the·data,·without·being·bound·to·them
336	explicitly).	336	explicitly).
337	Entire·simulation,·i.e.·both·data·and·functions,·are·stored·in·a·single·Scene	337	Entire·simulation,·i.e.·both·data·and·functions,·are·stored·in·a·single·Scene
338	object.·It·is·accessible·through·the·_\x8O_\x8m_\x8e_\x8g_\x8a·class·in·python·(a·singleton),·which	338	object.·It·is·accessible·through·the·_\x8O_\x8m_\x8e_\x8g_\x8a·class·in·python·(a·singleton),·which
339	is·by·default·stored·in·the·O·global·variable:	339	is·by·default·stored·in·the·O·global·variable:
340	Yade·[28]:·O.bodies·······#·some·data·components	340	Yade·[28]:·O.bodies·······#·some·data·components
341	Out[28]:·<yade.wrapper.BodyContainer·at·0xffff~~643~~1fa00>	341	Out[28]:·<yade.wrapper.BodyContainer·at·0xffff55f1fa70>

342	Yade·[29]:·len(O.bodies)··#·there·are·no·bodies·as·of·yet	342	Yade·[29]:·len(O.bodies)··#·there·are·no·bodies·as·of·yet
343	Out[29]:·0	343	Out[29]:·0

344	Yade·[30]:·O.engines······#·functional·components,·empty·at·the·moment	344	Yade·[30]:·O.engines······#·functional·components,·empty·at·the·moment
345	Out[30]:·[]	345	Out[30]:·[]
346	\x8\x8\x8·D\x8Da\x8at\x8ta\x8a·c\x8co\x8om\x8mp\x8po\x8on\x8ne\x8en\x8nt\x8ts\x8s_\x8?\x8¶·\x8\x8\x8	346	\x8\x8\x8·D\x8Da\x8at\x8ta\x8a·c\x8co\x8om\x8mp\x8po\x8on\x8ne\x8en\x8nt\x8ts\x8s_\x8?\x8¶·\x8\x8\x8
Offset 385, 17 lines modified		Offset 385, 17 lines modified
385	practical;·there·are·utility·functions·defined·to·create·them·with·all	385	practical;·there·are·utility·functions·defined·to·create·them·with·all
386	necessary·ingredients.·For·example,·we·can·create·sphere·particle·using	386	necessary·ingredients.·For·example,·we·can·create·sphere·particle·using
387	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8s_\x8p_\x8h_\x8e_\x8r_\x8e:	387	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8s_\x8p_\x8h_\x8e_\x8r_\x8e:
388	Yade·[31]:·s=utils.sphere(center=[0,0,0],radius=1)	388	Yade·[31]:·s=utils.sphere(center=[0,0,0],radius=1)

389	Yade·[32]:·s.shape,·s.state,·s.mat,·s.bound	389	Yade·[32]:·s.shape,·s.state,·s.mat,·s.bound
390	Out[32]:	390	Out[32]:
391	(<Sphere·instance·at·0x30~~491e9~~0>,	391	(<Sphere·instance·at·0x40f55040>,
392	·<State·instance·at·0x30~~56244~~0>,	392	·<State·instance·at·0x40fa9c70>,
393	·<FrictMat·instance·at·0x~~2ff2c94~~0>,	393	·<FrictMat·instance·at·0x40eca060>,
394	·None)	394	·None)

395	Yade·[33]:·s.state.pos	395	Yade·[33]:·s.state.pos
396	Out[33]:·Vector3(0,0,0)	396	Out[33]:·Vector3(0,0,0)

397	Yade·[34]:·s.shape.radius	397	Yade·[34]:·s.shape.radius
398	Out[34]:·1.0	398	Out[34]:·1.0
Offset 471, 29 lines modified		Offset 471, 29 lines modified
471	_\x8[_\x8__\x8i_\x8m_\x8a_\x8g_\x8e_\x8s_\x8/_\x8i_\x8n_\x8t_\x8e_\x8r_\x8a_\x8c_\x8t_\x8i_\x8o_\x8n_\x8-_\x8c_\x8l_\x8a_\x8s_\x8s_\x8e_\x8s_\x8._\x8p_\x8n_\x8g_\x8]	471	_\x8[_\x8__\x8i_\x8m_\x8a_\x8g_\x8e_\x8s_\x8/_\x8i_\x8n_\x8t_\x8e_\x8r_\x8a_\x8c_\x8t_\x8i_\x8o_\x8n_\x8-_\x8c_\x8l_\x8a_\x8s_\x8s_\x8e_\x8s_\x8._\x8p_\x8n_\x8g_\x8]
472	Examples·of·concrete·classes·that·might·be·used·to·describe·an·_\x8I_\x8n_\x8t_\x8e_\x8r_\x8a_\x8c_\x8t_\x8i_\x8o_\x8n:	472	Examples·of·concrete·classes·that·might·be·used·to·describe·an·_\x8I_\x8n_\x8t_\x8e_\x8r_\x8a_\x8c_\x8t_\x8i_\x8o_\x8n:
473	_\x8I_\x8G_\x8e_\x8o_\x8m,·_\x8G_\x8e_\x8n_\x8e_\x8r_\x8i_\x8c_\x8S_\x8p_\x8h_\x8e_\x8r_\x8e_\x8s_\x8C_\x8o_\x8n_\x8t_\x8a_\x8c_\x8t,·_\x8P_\x8o_\x8l_\x8y_\x8h_\x8e_\x8d_\x8r_\x8a_\x8G_\x8e_\x8o_\x8m,·_\x8C_\x8y_\x8l_\x8S_\x8c_\x8G_\x8e_\x8o_\x8m,·_\x8I_\x8P_\x8h_\x8y_\x8s,·_\x8N_\x8o_\x8r_\x8m_\x8P_\x8h_\x8y_\x8s,	473	_\x8I_\x8G_\x8e_\x8o_\x8m,·_\x8G_\x8e_\x8n_\x8e_\x8r_\x8i_\x8c_\x8S_\x8p_\x8h_\x8e_\x8r_\x8e_\x8s_\x8C_\x8o_\x8n_\x8t_\x8a_\x8c_\x8t,·_\x8P_\x8o_\x8l_\x8y_\x8h_\x8e_\x8d_\x8r_\x8a_\x8G_\x8e_\x8o_\x8m,·_\x8C_\x8y_\x8l_\x8S_\x8c_\x8G_\x8e_\x8o_\x8m,·_\x8I_\x8P_\x8h_\x8y_\x8s,·_\x8N_\x8o_\x8r_\x8m_\x8P_\x8h_\x8y_\x8s,
474	_\x8N_\x8o_\x8r_\x8m_\x8S_\x8h_\x8e_\x8a_\x8r_\x8P_\x8h_\x8y_\x8s,·_\x8F_\x8r_\x8i_\x8c_\x8t_\x8P_\x8h_\x8y_\x8s._\x8¶	474	_\x8N_\x8o_\x8r_\x8m_\x8S_\x8h_\x8e_\x8a_\x8r_\x8P_\x8h_\x8y_\x8s,·_\x8F_\x8r_\x8i_\x8c_\x8t_\x8P_\x8h_\x8y_\x8s._\x8¶
475	Suppose·now·interactions·have·been·already·created.·We·can·access·them·by·the	475	Suppose·now·interactions·have·been·already·created.·We·can·access·them·by·the
476	id·pair:	476	id·pair:
477	Yade·[41]:·O.interactions[0,1]	477	Yade·[41]:·O.interactions[0,1]
478	Out[41]:·<Interaction·instance·at·0x30~~4ec93~~0>	478	Out[41]:·<Interaction·instance·at·0x40f93450>

479	Yade·[42]:·O.interactions[1,0]·····#·order·of·ids·is·not·important	479	Yade·[42]:·O.interactions[1,0]·····#·order·of·ids·is·not·important
480	Out[42]:·<Interaction·instance·at·0x30~~4ec93~~0>	480	Out[42]:·<Interaction·instance·at·0x40f93450>

481	Yade·[43]:·i=O.interactions[0,1]	481	Yade·[43]:·i=O.interactions[0,1]

482	Yade·[44]:·i.id1,i.id2	482	Yade·[44]:·i.id1,i.id2
483	Out[44]:·(0,·1)	483	Out[44]:·(0,·1)

484	Yade·[45]:·i.geom	484	Yade·[45]:·i.geom
485	Out[45]:·<ScGeom·instance·at·0x30~~4cd80~~0>	485	Out[45]:·<ScGeom·instance·at·0x40f31a80>

486	Yade·[46]:·i.phys	486	Yade·[46]:·i.phys
487	Out[46]:·<FrictPhys·instance·at·0x2ff~~0a22~~0>	487	Out[46]:·<FrictPhys·instance·at·0x40f388c0>

488	Yade·[47]:·O.interactions[100,10111]·····#·asking·for·non·existing·interaction	488	Yade·[47]:·O.interactions[100,10111]·····#·asking·for·non·existing·interaction
489	throws·exception	489	throws·exception
490	[0;31m-------------------------------------------------------------------------	490	[0;31m-------------------------------------------------------------------------
491	--\x1b[0m	491	--\x1b[0m
492	[0;31mIndexError\x1b[0m································Traceback·(most·recent·call	492	[0;31mIndexError\x1b[0m································Traceback·(most·recent·call
493	last)	493	last)

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+YN\x147;R܀\\x3\x1cǞJ\x7)\)fR
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+\x1e}}\x1b\x11\x12\x5bk~L@>L\x6Z)\xc[~𡃊Q3y)q\x1c·I»      \x11Z\x11gȭ(O`88\x1e\x18vݹQruGTǼmQ>J\xb؋\x16» V3wAR/x8|r\xc\x19l.\x18V\x6*\x11\xcPGjjTs?ݠ\xe+O[O76:·9.eq\x5Mzbq>ǎ8y_\x14a\xbgJoI\x19%e?n&N&vdgCQ\x17o)c*stiҴw3^f\x14a԰hkϔg\x85\x16z"ww@\x12>\xf$\x15jk`aַֈ4[-\xfet\xcxg~#\x7֊MKH\x1fHE3\x14kA\x3I·G,\x16lSلBC\xf+\h]3ퟛGuC|+\x12z\x0fk]DWvMtXoR8;H\x16I!\x5~lhyJ%\x12\x15\x1fT\xfFڞ\aI[[4q\x13̫9\x18sn)L\x19l\x3le!\x16!"26oSCz?(\xb$N
+C)$*4\xe>6H$\x5d\xd\x1d»޵R7#$4mO_\x17u_:w5vK\x13GX\x51\xfloM)w:^SRUGSTA%\x1dVW\x115»     :)\x1cQSS<\x17\x18Yv/&K\x16\x19*MH\x1eFOz\xd\x6ͨ6&·D_|_1Ng>M.1b:Lf\x1d\»      !\x16ǲlT֐;A9򄴫!y·6\x1d\x19Ӈ(·l\x120}\x4*f7)\xf\x1ej\x5
+U,\x17e
+\xcUbYnZ^\x7MʴTT4e8Jy9*\x7˃Zc\x152d5CO6J\xfRc\x15\x1aډR5CIl2]H\x14먆\x16^UP"
+RsxlTXfD녻Z»     <Q6Q+S\x14븞Sޮ\x17\x19\xb1}?{ݏ*\x19c<\x115Մe
+GdHO3m0n|ɧ$rx\V@\x1d2\x16\xf?VL>B\x1ah{hE\x14r跈Ob
+<w7R\x1cr·}ZN]/pr\tBkւ\x14P͜XY%\x7\x14F\x1b;\x7~Ҿ4<-{dM܋\xf\xfI[\xdGg
+\x17eϛ\x1f}z7_?ܿ\x49+\x16<<͎\x4͹K;\xd\xcgm\xdcp\x7sx_W߸\x198\xe:\x4:9\x12چ\x1fY[CH\x16tla
+{킍\x1c7\xeXS\x0\x3_D\x1f-»      z\xbV\x4ؠ\xe[<#\x7\x3¥\x16\x17Z8|AҙX\xbǈW\x17\x84*`[\x0qWT


Offset 1094, 19 lines modified		Offset 1094, 19 lines modified
1094	<trackEnergy>0</trackEnergy>	1094	<trackEnergy>0</trackEnergy>
1095	<doSort>0</doSort>	1095	<doSort>0</doSort>
1096	<runInternalConsistencyChecks>1</runInternalConsistencyChecks>	1096	<runInternalConsistencyChecks>1</runInternalConsistencyChecks>
1097	<selectedBody>-1</selectedBody>	1097	<selectedBody>-1</selectedBody>
1098	<tags·class_id="3"·tracking_level="0"·version="0">	1098	<tags·class_id="3"·tracking_level="0"·version="0">
1099	<count>5</count>	1099	<count>5</count>
1100	<item_version>0</item_version>	1100	<item_version>0</item_version>
1101	<item>author=~(pbuilder1@codeth~~ink04-ar~~m64)</item>	1101	<item>author=second~user~(pbuilder2@i-capture-the-hostname)</item>
1102	<item>isoTime=20250~~727~~T~~113446~~</item>	1102	<item>isoTime=20260831T035003</item>
1103	<item>id=20250727T113446p3257836</item>
1104	<item>d.id=20250727T113446p3257836</item>
1105	<item>id.d=20250~~727~~T~~113446~~p32~~57836~~</item>	1103	<item>id=20260831T035003p363122</item>
		1104	<item>d.id=20260831T035003p363122</item>
		1105	<item>id.d=20260831T035003p363122</item>
1106	</tags>	1106	</tags>
1107	<engines·class_id="4"·tracking_level="0"·version="0">	1107	<engines·class_id="4"·tracking_level="0"·version="0">
1108	<count>1</count>	1108	<count>1</count>
1109	<item_version>1</item_version>	1109	<item_version>1</item_version>
1110	<item·class_id="5"·tracking_level="0"·version="1">	1110	<item·class_id="5"·tracking_level="0"·version="1">
1111	<px·class_id="7"·class_name="yade::GravityEngine"·tracking_level="1"	1111	<px·class_id="7"·class_name="yade::GravityEngine"·tracking_level="1"
1112	version="0"·object_id="_2">	1112	version="0"·object_id="_2">
Offset 1821, 15 lines modified		Offset 1821, 15 lines modified
1821	Yade·[42]:·ld=LawDispatcher([Law2_ScGeom_CpmPhys_Cpm()])	1821	Yade·[42]:·ld=LawDispatcher([Law2_ScGeom_CpmPhys_Cpm()])

1822	Yade·[43]:·ld.dispMatrix()	1822	Yade·[43]:·ld.dispMatrix()
1823	Out[43]:·{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}	1823	Out[43]:·{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}

1824	#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request	1824	#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request
1825	Yade·[44]:·ld.dispFunctor(ScGridCoGeom(),CpmPhys())	1825	Yade·[44]:·ld.dispFunctor(ScGridCoGeom(),CpmPhys())
1826	Out[44]:·<Law2_ScGeom_CpmPhys_Cpm·instance·at·0x30~~56e62~~0>	1826	Out[44]:·<Law2_ScGeom_CpmPhys_Cpm·instance·at·0x40fb2240>

1827	Yade·[45]:·ld.dispMatrix()	1827	Yade·[45]:·ld.dispMatrix()
1828	Out[45]:	1828	Out[45]:
1829	{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',	1829	{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',
1830	·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}	1830	·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}
1831	\x8\x8\x8·O\x8Op\x8pe\x8en\x8nG\x8GL\x8L·f\x8fu\x8un\x8nc\x8ct\x8to\x8or\x8rs\x8s_\x8?\x8¶·\x8\x8\x8	1831	\x8\x8\x8·O\x8Op\x8pe\x8en\x8nG\x8GL\x8L·f\x8fu\x8un\x8nc\x8ct\x8to\x8or\x8rs\x8s_\x8?\x8¶·\x8\x8\x8
1832	OpenGL·rendering·is·being·done·also·by·1D·functors·(dispatched·for·the·type·to	1832	OpenGL·rendering·is·being·done·also·by·1D·functors·(dispatched·for·the·type·to
Offset 1961, 39 lines modified		Offset 1961, 39 lines modified
1961	Yade·[52]:·O.run(50);·O.wait()	1961	Yade·[52]:·O.run(50);·O.wait()

1962	Yade·[53]:·yade.timing.stats()	1962	Yade·[53]:·yade.timing.stats()
1963	Name····················································Count	1963	Name····················································Count
1964	Time············Rel.·time	1964	Time············Rel.·time
1965	-------------------------------------------------------------------------------	1965	-------------------------------------------------------------------------------
1966	------------------------	1966	------------------------
1967	"firstEngine"········································50·············~~92.~~161us	1967	"firstEngine"········································50···············91.8us
1968	0.56%	1968	0.56%
1969	InsertionSortCollider································25············4~~544~~.47us	1969	InsertionSortCollider································25············4611.52us
1970	27.66%	1970	27.95%
1971	InteractionLoop······································50···········8288.258us	1971	InteractionLoop······································50············8297.32us
1972	50.45%	1972	50.28%
1973	GlobalStiffnessTimeStepper····························2··············50.44us	1973	GlobalStiffnessTimeStepper····························2··············51.48us
1974	0.31%	1974	0.31%
1975	TriaxialCompressionEngine····························50···········1111.245us	1975	TriaxialCompressionEngine····························50············1127.84us
1976	6.76%	1976	6.83%
1977	TriaxialStateRecorder·································3············303~~.602~~us	1977	TriaxialStateRecorder·································3··············335.6us
1978	1.85%	1978	2.03%
1979	NewtonIntegrator·····································50···········~~2037.972~~us	1979	NewtonIntegrator·····································50············1985.68us
1980	12.41%	1980	12.03%
1981	··forces·sync··········································50··············25.08us	1981	··forces·sync··········································50··············23.16us
1982	1.23%	1982	1.17%
1983	··motion·integration···································50···········1~~950~~.292us	1983	··motion·integration···································50············1899.84us
1984	95.70%	1984	95.68%
1985	··sync·max·vel·········································50··············16.12us	1985	··sync·max·vel·········································50··············15.48us
1986	0.79%	1986	0.78%
1987	··terminate············································50···············8.96us	1987	··terminate············································50···············8.56us
1988	0.44%	1988	0.43%
1989	··TOTAL···············································200···········~~2000.452~~us	1989	··TOTAL···············································200············1947.04us
1990	98.16%	1990	98.05%
1991	TOTAL····························································16~~428~~.148us	1991	TOTAL·····························································16501.24us
1992	100.00%	1992	100.00%
1993	Exec·count·and·time·can·be·accessed·and·manipulated·through·Engine::timingInfo	1993	Exec·count·and·time·can·be·accessed·and·manipulated·through·Engine::timingInfo
1994	from·c++·or·Engine().execCount·and·Engine().execTime·properties·in·Python.	1994	from·c++·or·Engine().execCount·and·Engine().execTime·properties·in·Python.
1995	\x8\x8\x8·I\x8In\x8n-\x8-e\x8en\x8ng\x8gi\x8in\x8ne\x8e·a\x8an\x8nd\x8d·i\x8in\x8n-\x8-f\x8fu\x8un\x8nc\x8ct\x8to\x8or\x8r·t\x8ti\x8im\x8mi\x8in\x8ng\x8g_\x8?\x8¶·\x8\x8\x8	1995	\x8\x8\x8·I\x8In\x8n-\x8-e\x8en\x8ng\x8gi\x8in\x8ne\x8e·a\x8an\x8nd\x8d·i\x8in\x8n-\x8-f\x8fu\x8un\x8nc\x8ct\x8to\x8or\x8r·t\x8ti\x8im\x8mi\x8in\x8ng\x8g_\x8?\x8¶·\x8\x8\x8
1996	Timing·within·engines·(and·functors)·is·based·on·_\x8T_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·class·which·is·by	1996	Timing·within·engines·(and·functors)·is·based·on·_\x8T_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·class·which·is·by
1997	default·instantiated·in·engines·and·functors·as·Engine::timingDeltas·and	1997	default·instantiated·in·engines·and·functors·as·Engine::timingDeltas·and
1998	Functor::timingDeltas·(_\x8E_\x8n_\x8g_\x8i_\x8n_\x8e_\x8._\x8t_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·and·_\x8F_\x8u_\x8n_\x8c_\x8t_\x8o_\x8r_\x8._\x8t_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·in·Python).	1998	Functor::timingDeltas·(_\x8E_\x8n_\x8g_\x8i_\x8n_\x8e_\x8._\x8t_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·and·_\x8F_\x8u_\x8n_\x8c_\x8t_\x8o_\x8r_\x8._\x8t_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·in·Python).


Offset 62408, 15 lines modified		Offset 62408, 15 lines modified
62408	········"023":·28,	62408	········"023":·28,
62409	········"02319":·33,	62409	········"02319":·33,
62410	········"024":·28,	62410	········"024":·28,
62411	········"0242":·28,	62411	········"0242":·28,
62412	········"02622":·28,	62412	········"02622":·28,
62413	········"02644400910985170":·28,	62413	········"02644400910985170":·28,
62414	········"029":·28,	62414	········"029":·28,
62415	········"03":·[28,·29,·33,·47,·66],	62415	········"03":·[27,·28,·29,·33,·47,·66],
62416	········"031":·28,	62416	········"031":·28,
62417	········"031304":·29,	62417	········"031304":·29,
62418	········"032901":·28,	62418	········"032901":·28,
62419	········"03333":·33,	62419	········"03333":·33,
62420	········"034":·28,	62420	········"034":·28,
62421	········"0352":·28,	62421	········"0352":·28,
62422	········"0374":·28,	62422	········"0374":·28,
Offset 62430, 15 lines modified		Offset 62430, 16 lines modified
62430	········"04024029":·28,	62430	········"04024029":·28,
62431	········"04024060":·28,	62431	········"04024060":·28,
62432	········"04024079":·28,	62432	········"04024079":·28,
62433	········"041":·28,	62433	········"041":·28,
62434	········"041301":·28,	62434	········"041301":·28,
62435	········"0423":·28,	62435	········"0423":·28,
62436	········"0471975511965976":·47,	62436	········"0471975511965976":·47,
		62437	········"04u":·27,
62437	········"05":·[28,·29,·31,·32,·33,·34,·46,·47,·60,·67],	62438	········"05":·[27,·28,·29,·31,·32,·33,·34,·46,·47,·60,·67],
62438	········"0500":·28,	62439	········"0500":·28,
62439	········"051":·28,	62440	········"051":·28,
62440	········"052":·28,	62441	········"052":·28,
62441	········"0527":·28,	62442	········"0527":·28,
62442	········"052905":·[28,·33],	62443	········"052905":·[28,·33],
62443	········"0530":·60,	62444	········"0530":·60,
62444	········"0558":·28,	62445	········"0558":·28,
Offset 62461, 15 lines modified		Offset 62462, 14 lines modified
62461	········"0733":·29,	62462	········"0733":·29,
62462	········"0740":·28,	62463	········"0740":·28,
62463	········"0785":·28,	62464	········"0785":·28,
62464	········"08":·[27,·28,·29,·47,·59,·65],	62465	········"08":·[27,·28,·29,·47,·59,·65],
62465	········"0815":·28,	62466	········"0815":·28,
62466	········"08927029208022474":·29,	62467	········"08927029208022474":·29,
62467	········"08927029908022097":·29,	62468	········"08927029908022097":·29,
62468	········"08u":·27,
62469	········"09":·[28,·29,·65],	62469	········"09":·[28,·29,·65],
62470	········"090192":·29,	62470	········"090192":·29,
62471	········"09057":·28,	62471	········"09057":·28,
62472	········"0b000011":·[60,·67],	62472	········"0b000011":·[60,·67],
62473	········"0b011":·34,	62473	········"0b011":·34,
62474	········"0b100101":·60,	62474	········"0b100101":·60,
62475	········"0b1101":·60,	62475	········"0b1101":·60,
Offset 62486, 35 lines modified		Offset 62486, 35 lines modified
62486	········"0x00007f0fcd0b4b23":·47,	62486	········"0x00007f0fcd0b4b23":·47,
62487	········"0x00007f0fcd87ed57":·47,	62487	········"0x00007f0fcd87ed57":·47,
62488	········"0x00007f0fcd88c7e9":·47,	62488	········"0x00007f0fcd88c7e9":·47,
62489	········"0x00007f0fcd88cb20":·47,	62489	········"0x00007f0fcd88cb20":·47,
62490	········"0x00007f0fcd8f4f7d":·47,	62490	········"0x00007f0fcd8f4f7d":·47,
62491	········"0x1c54620":·47,	62491	········"0x1c54620":·47,
62492	········"0x2d06770":·27,	62492	········"0x2d06770":·27,
62493	········"0x2e918390":·66,
62494	········"0x2ff0a220":·23,
62495	········"0x2ff2c940":·23,
62496	········"0x30491e90":·23,
62497	········"0x304b~~3a0~~0":·35,	62493	········"0x3e7b0ba0":·47,
		62494	········"0x3f362eb0":·66,
		62495	········"0x405f1d50":·43,
62498	········"0x304c~~d80~~0":·23,	62496	········"0x40eca060":·23,
		62497	········"0x40f04940":·47,
		62498	········"0x40f31a80":·23,
62499	········"0x30~~4ec93~~0":·23,	62499	········"0x40f388c0":·23,
62500	········"0x30~~5624~~40":·23,	62500	········"0x40f55040":·23,
		62501	········"0x40f93450":·23,
		62502	········"0x40fa9c70":·23,
62501	········"0x30~~56e62~~0":·27,	62503	········"0x40fb2240":·27,
62502	········"0x305e5ff0":·35,
62503	········"0x30~~63f2~~70":·35,	62504	········"0x40fdea70":·35,
62504	········"0x3~~066~~34b0":·43,	62505	········"0x41034de0":·35,
62505	········"0x306768a0":·35,
62506	········"0x306b4510":·35,	62506	········"0x4109bed0":·35,
		62507	········"0x41119970":·35,
		62508	········"0x41147dd0":·35,
		62509	········"0x41147e70":·43,
62507	········"0x~~3070083~~0":·43,	62510	········"0x4132c900":·43,
62508	········"0x~~308dc16~~0":·43,	62511	········"0x4134dd70":·47,
62509	········"0x~~308e46~~60":·43,	62512	········"0x4134f460":·43,
62510	········"0x30908230":·47,
62511	········"0x3090f3e0":·47,
62512	········"0x~~30910e3~~0":·43,	62513	········"0x4136a000":·43,
62513	········"0x30922500":·47,
62514	········"0x7f0fb1268710":·47,	62514	········"0x7f0fb1268710":·47,
62515	········"0x7f0fb29f2710":·47,	62515	········"0x7f0fb29f2710":·47,
62516	········"0x7f0fb31f3710":·47,	62516	········"0x7f0fb31f3710":·47,
62517	········"0x7f0fcee53700":·47,	62517	········"0x7f0fcee53700":·47,
62518	········"0x7f1e4231e440":·25,	62518	········"0x7f1e4231e440":·25,
62519	········"0x7f20086a1490":·25,	62519	········"0x7f20086a1490":·25,
62520	········"0x7f21a8c8d3a0":·25,	62520	········"0x7f21a8c8d3a0":·25,
Offset 62523, 39 lines modified		Offset 62523, 39 lines modified
62523	········"0x7f622b47f490":·25,	62523	········"0x7f622b47f490":·25,
62524	········"0x7f8dc7b73440":·25,	62524	········"0x7f8dc7b73440":·25,
62525	········"0x7f9231213490":·25,	62525	········"0x7f9231213490":·25,
62526	········"0x7f9c0a399490":·25,	62526	········"0x7f9c0a399490":·25,
62527	········"0x7fb699b1a440":·25,	62527	········"0x7fb699b1a440":·25,
62528	········"0x7fdd466b8440":·25,	62528	········"0x7fdd466b8440":·25,
62529	········"0x7feb979403a0":·25,	62529	········"0x7feb979403a0":·25,
62530	········"0xffff~~643~~1fa00":·23,	62530	········"0xffff55f1fa70":·23,
62531	········"0xffff7~~a4b7~~820":·47,	62531	········"0xffff70143820":·47,
62532	········"0xffff7~~a4f7~~380":·47,	62532	········"0xffff7018b380":·47,
62533	········"0xffff7~~a52~~a570":·47,	62533	········"0xffff701ba570":·47,
62534	········"0xffff7~~a56~~9810":·47,	62534	········"0xffff701f9810":·47,
62535	········"0xffff7~~a56~~9950":·47,	62535	········"0xffff701f9950":·47,
62536	········"0xffff7~~a58~~c180":·47,	62536	········"0xffff7021c180":·47,
62537	········"1":·[0,·1,·2,·3,·4,·5,·6,·13,·14,·16,·22,·23,·25,·26,·27,·28,·29,·32,·33,·34,·35,·39,·43,·46,·47,·48,·49,·50,·51,·52,·53,·54,·55,·56,·57,·58,·59,·60,·62,·63,·65,·66,·67,·68,·69],	62537	········"1":·[0,·1,·2,·3,·4,·5,·6,·13,·14,·16,·22,·23,·25,·26,·27,·28,·29,·32,·33,·34,·35,·39,·43,·46,·47,·48,·49,·50,·51,·52,·53,·54,·55,·56,·57,·58,·59,·60,·62,·63,·65,·66,·67,·68,·69],
62538	········"10":·[0,·1,·2,·3,·4,·5,·7,·13,·22,·23,·25,·26,·27,·28,·29,·33,·34,·35,·41,·43,·45,·46,·47,·50,·51,·56,·59,·60,·63,·66,·67,·69],	62538	········"10":·[0,·1,·2,·3,·4,·5,·7,·13,·22,·23,·25,·26,·27,·28,·29,·33,·34,·35,·41,·43,·45,·46,·47,·50,·51,·56,·59,·60,·63,·66,·67,·69],
62539	········"100":·[6,·23,·25,·27,·32,·33,·34,·35,·41,·45,·46,·47,·65],	62539	········"100":·[6,·23,·25,·27,·32,·33,·34,·35,·41,·45,·46,·47,·65],
62540	········"1000":·[1,·23,·26,·32,·33,·34,·41,·44,·45,·46,·47,·56,·60,·66,·67],	62540	········"1000":·[1,·23,·26,·32,·33,·34,·41,·44,·45,·46,·47,·56,·60,·66,·67],
62541	········"10000":·[33,·41,·56,·60,·67],	62541	········"10000":·[33,·41,·56,·60,·67],
62542	········"100000":·23,	62542	········"100000":·23,
62543	········"1000000":·3,	62543	········"1000000":·3,
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62545	········"100068":·28,	62545	········"100068":·28,
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62547	········"10011101011100001010001111010111000010100011110101110":·3,	62547	········"10011101011100001010001111010111000010100011110101110":·3,
62548	········"10011101011100001010001111010111000010100011110101110000000000000000000000000000000000000000000000000000000000000":·3,	62548	········"10011101011100001010001111010111000010100011110101110000000000000000000000000000000000000000000000000000000000000":·3,
62549	········"10011101011100001010001111010111000010100011110101110000101000111101011100001010001111010111000010100011110101110":·3,	62549	········"10011101011100001010001111010111000010100011110101110000101000111101011100001010001111010111000010100011110101110":·3,
62550	········"1002":·[28,·29,·60,·67],	62550	········"1002":·[28,·29,·60,·67],
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62552	········"1006":·29,	62551	········"1006":·29,
62553	········"1007":·[28,·29],	62552	········"1007":·[28,·29],
62554	········"10070737":·28,	62553	········"10070737":·28,
		62554	········"100723":·23,
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Offset 225, 18 lines modified		Offset 225, 18 lines modified
225	<p>Periodic·boundary·is·a·“boundary”·created·by·using·periodic·(rather·than·infinite)·space.·Such·boundary·is·activated·by·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.periodic">O.periodic=True·</a>,·and·the·space·configuration·is·decribed·by·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.cell">O.cell·</a>.·It·is·well·suited·for·studying·bulk·material·behavior,·as·boundary·effects·are·avoided,·leading·to·smaller·number·of·particles.·On·the·other·hand,·it·might·not·be·suitable·for·studying·localization,·as·any·cell-level·effects·(such·as·shear·bands)·have·to·satisfy·periodicity·as·well.</p>	225	<p>Periodic·boundary·is·a·“boundary”·created·by·using·periodic·(rather·than·infinite)·space.·Such·boundary·is·activated·by·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.periodic">O.periodic=True·</a>,·and·the·space·configuration·is·decribed·by·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.cell">O.cell·</a>.·It·is·well·suited·for·studying·bulk·material·behavior,·as·boundary·effects·are·avoided,·leading·to·smaller·number·of·particles.·On·the·other·hand,·it·might·not·be·suitable·for·studying·localization,·as·any·cell-level·effects·(such·as·shear·bands)·have·to·satisfy·periodicity·as·well.</p>
226	<p>The·periodic·cell·is·described·by·its·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.refSize">reference·size·</a>·of·box·aligned·with·global·axes,·and·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.trsf">current·transformation</a>,·which·can·capture·stretch,·shear·and·rotation.·Deformation·is·prescribed·via·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.velGrad">velocity·gradient</a>,·which·updates·the·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.trsf">transformation</a>·before·the·next·step.·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.homoDeform">Homothetic·deformation</a>·can·smear·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.velGrad">velocity·gradient</a>·accross·the·cell,·making·the·boundary·dissolve·in·the·whole·cell.</p>	226	<p>The·periodic·cell·is·described·by·its·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.refSize">reference·size·</a>·of·box·aligned·with·global·axes,·and·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.trsf">current·transformation</a>,·which·can·capture·stretch,·shear·and·rotation.·Deformation·is·prescribed·via·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.velGrad">velocity·gradient</a>,·which·updates·the·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.trsf">transformation</a>·before·the·next·step.·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.homoDeform">Homothetic·deformation</a>·can·smear·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Cell.velGrad">velocity·gradient</a>·accross·the·cell,·making·the·boundary·dissolve·in·the·whole·cell.</p>
227	<p>Stress·and·strains·can·be·controlled·with·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController">PeriTriaxController</a>;·it·is·possible·to·prescribe·mixed·strain/stress·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.goal">goal</a>·state·using·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.stressMask">PeriTriaxController.stressMask</a>.</p>	227	<p>Stress·and·strains·can·be·controlled·with·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController">PeriTriaxController</a>;·it·is·possible·to·prescribe·mixed·strain/stress·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.goal">goal</a>·state·using·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.stressMask">PeriTriaxController.stressMask</a>.</p>
228	<p>The·following·creates·periodic·cloud·of·spheres·and·compresses·to·achieve·<span·class="math·notranslate·nohighlight">\(\sigma_x\)</span>=-10·kPa,·<span·class="math·notranslate·nohighlight">\(\sigma_y\)</span>=-10kPa·and·<span·class="math·notranslate·nohighlight">\(\eps_z\)</span>=-0.1.·Since·stress·is·specified·for·<span·class="math·notranslate·nohighlight">\(y\)</span>·and·<span·class="math·notranslate·nohighlight">\(z\)</span>,·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.stressMask">stressMask</a>·is·binary·<code·class="docutils·literal·notranslate"><span·class="pre">0b011</span></code>·(x→1,·y→2,·z→4,·in·decimal·1+2=3).</p>	228	<p>The·following·creates·periodic·cloud·of·spheres·and·compresses·to·achieve·<span·class="math·notranslate·nohighlight">\(\sigma_x\)</span>=-10·kPa,·<span·class="math·notranslate·nohighlight">\(\sigma_y\)</span>=-10kPa·and·<span·class="math·notranslate·nohighlight">\(\eps_z\)</span>=-0.1.·Since·stress·is·specified·for·<span·class="math·notranslate·nohighlight">\(y\)</span>·and·<span·class="math·notranslate·nohighlight">\(z\)</span>,·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.stressMask">stressMask</a>·is·binary·<code·class="docutils·literal·notranslate"><span·class="pre">0b011</span></code>·(x→1,·y→2,·z→4,·in·decimal·1+2=3).</p>
229	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[1]:·</span><span·class="n">sp</span><span·class="o">=</span><span·class="n">pack</span><span·class="o">.</span><span·class="n">SpherePack</span><span·class="p">()</span>	229	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[1]:·</span><span·class="n">sp</span><span·class="o">=</span><span·class="n">pack</span><span·class="o">.</span><span·class="n">SpherePack</span><span·class="p">()</span>

230	<span·class="gp">Yade·[2]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">makeCloud</span><span·class="p">((</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">),(</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">),</span><span·class="n">rMean</span><span·class="o">=</span><span·class="mf">.16</span><span·class="p">,</span><span·class="n">periodic</span><span·class="o">=</span><span·class="kc">True</span><span·class="p">)</span>	230	<span·class="gp">Yade·[2]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">makeCloud</span><span·class="p">((</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">),(</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">),</span><span·class="n">rMean</span><span·class="o">=</span><span·class="mf">.16</span><span·class="p">,</span><span·class="n">periodic</span><span·class="o">=</span><span·class="kc">True</span><span·class="p">)</span>
231	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">2</span><span·class="p">]:</span>·<span·class="mi">19</span>	231	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">2</span><span·class="p">]:</span>·<span·class="mi">18</span>

232	<span·class="gp">Yade·[3]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">toSimulation</span><span·class="p">()</span>·············<span·class="c1">#·implicitly·sets·O.periodic=True,·and·O.cell.refSize·to·the·packing·period·size</span>	232	<span·class="gp">Yade·[3]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">toSimulation</span><span·class="p">()</span>·············<span·class="c1">#·implicitly·sets·O.periodic=True,·and·O.cell.refSize·to·the·packing·period·size</span>
233	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">3</span><span·class="p">]:</span>·<span·class="p">[</span><span·class="mi">4</span><span·class="p">,</span>·<span·class="mi">5</span><span·class="p">,</span>·<span·class="mi">6</span><span·class="p">,</span>·<span·class="mi">7</span><span·class="p">,</span>·<span·class="mi">8</span><span·class="p">,</span>·<span·class="mi">9</span><span·class="p">,</span>·<span·class="mi">10</span><span·class="p">,</span>·<span·class="mi">11</span><span·class="p">,</span>·<span·class="mi">12</span><span·class="p">,</span>·<span·class="mi">13</span><span·class="p">,</span>·<span·class="mi">14</span><span·class="p">,</span>·<span·class="mi">15</span><span·class="p">,</span>·<span·class="mi">16</span><span·class="p">,</span>·<span·class="mi">17</span><span·class="p">,</span>·<span·class="mi">18</span><span·class="p">,</span>·<span·class="mi">19</span><span·class="p">,</span>·<span·class="mi">20</span><span·class="p">,</span>·<span·class="mi">21</span><span·class="p">~~,</span>·<span·class="mi">22</span><span·class="p">~~]</span>	233	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">3</span><span·class="p">]:</span>·<span·class="p">[</span><span·class="mi">4</span><span·class="p">,</span>·<span·class="mi">5</span><span·class="p">,</span>·<span·class="mi">6</span><span·class="p">,</span>·<span·class="mi">7</span><span·class="p">,</span>·<span·class="mi">8</span><span·class="p">,</span>·<span·class="mi">9</span><span·class="p">,</span>·<span·class="mi">10</span><span·class="p">,</span>·<span·class="mi">11</span><span·class="p">,</span>·<span·class="mi">12</span><span·class="p">,</span>·<span·class="mi">13</span><span·class="p">,</span>·<span·class="mi">14</span><span·class="p">,</span>·<span·class="mi">15</span><span·class="p">,</span>·<span·class="mi">16</span><span·class="p">,</span>·<span·class="mi">17</span><span·class="p">,</span>·<span·class="mi">18</span><span·class="p">,</span>·<span·class="mi">19</span><span·class="p">,</span>·<span·class="mi">20</span><span·class="p">,</span>·<span·class="mi">21</span><span·class="p">]</span>

234	<span·class="gp">Yade·[4]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span><span·class="o">+=</span><span·class="p">[</span><span·class="n">PeriTriaxController</span><span·class="p">(</span><span·class="n">goal</span><span·class="o">=</span><span·class="p">(</span><span·class="o">-</span><span·class="mf">1e4</span><span·class="p">,</span><span·class="o">-</span><span·class="mf">1e4</span><span·class="p">,</span><span·class="o">-</span><span·class="mf">.1</span><span·class="p">),</span><span·class="n">stressMask</span><span·class="o">=</span><span·class="mb">0b011</span><span·class="p">,</span><span·class="n">maxUnbalanced</span><span·class="o">=</span><span·class="mf">.2</span><span·class="p">,</span><span·class="n">doneHook</span><span·class="o">=</span><span·class="s1">'functionToRunWhenFinished()'</span><span·class="p">)]</span>	234	<span·class="gp">Yade·[4]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span><span·class="o">+=</span><span·class="p">[</span><span·class="n">PeriTriaxController</span><span·class="p">(</span><span·class="n">goal</span><span·class="o">=</span><span·class="p">(</span><span·class="o">-</span><span·class="mf">1e4</span><span·class="p">,</span><span·class="o">-</span><span·class="mf">1e4</span><span·class="p">,</span><span·class="o">-</span><span·class="mf">.1</span><span·class="p">),</span><span·class="n">stressMask</span><span·class="o">=</span><span·class="mb">0b011</span><span·class="p">,</span><span·class="n">maxUnbalanced</span><span·class="o">=</span><span·class="mf">.2</span><span·class="p">,</span><span·class="n">doneHook</span><span·class="o">=</span><span·class="s1">'functionToRunWhenFinished()'</span><span·class="p">)]</span>
235	</pre></div>	235	</pre></div>
236	</div>	236	</div>
237	<p>When·the·simulation·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.run">runs</a>,·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController">PeriTriaxController</a>·takes·over·the·control·and·calls·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.doneHook">doneHook</a>·when·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.goal">goal</a>·is·reached.·A·full·simulation·with·PeriTriaxController·might·look·like·the·following:</p>	237	<p>When·the·simulation·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.run">runs</a>,·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController">PeriTriaxController</a>·takes·over·the·control·and·calls·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.doneHook">doneHook</a>·when·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.PeriTriaxController.goal">goal</a>·is·reached.·A·full·simulation·with·PeriTriaxController·might·look·like·the·following:</p>
238	<div·class="highlight-default·notranslate"><div·class="highlight"><pre><span></span><span·class="kn">from</span>·<span·class="nn">yade</span>·<span·class="kn">import</span>·<span·class="n">pack</span><span·class="p">,</span>·<span·class="n">plot</span>	238	<div·class="highlight-default·notranslate"><div·class="highlight"><pre><span></span><span·class="kn">from</span>·<span·class="nn">yade</span>·<span·class="kn">import</span>·<span·class="n">pack</span><span·class="p">,</span>·<span·class="n">plot</span>


Offset 122, 19 lines modified		Offset 122, 19 lines modified
122	The·following·creates·periodic·cloud·of·spheres·and·compresses·to·achieve·\	122	The·following·creates·periodic·cloud·of·spheres·and·compresses·to·achieve·\
123	(\sigma_x\)=-10·kPa,·\(\sigma_y\)=-10kPa·and·\(\eps_z\)=-0.1.·Since·stress·is	123	(\sigma_x\)=-10·kPa,·\(\sigma_y\)=-10kPa·and·\(\eps_z\)=-0.1.·Since·stress·is
124	specified·for·\(y\)·and·\(z\),·_\x8s_\x8t_\x8r_\x8e_\x8s_\x8s_\x8M_\x8a_\x8s_\x8k·is·binary·0b011·(x→1,·y→2,·z→4,·in	124	specified·for·\(y\)·and·\(z\),·_\x8s_\x8t_\x8r_\x8e_\x8s_\x8s_\x8M_\x8a_\x8s_\x8k·is·binary·0b011·(x→1,·y→2,·z→4,·in
125	decimal·1+2=3).	125	decimal·1+2=3).
126	Yade·[1]:·sp=pack.SpherePack()	126	Yade·[1]:·sp=pack.SpherePack()

127	Yade·[2]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.16,periodic=True)	127	Yade·[2]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.16,periodic=True)
128	Out[2]:·19	128	Out[2]:·18

129	Yade·[3]:·sp.toSimulation()·············#·implicitly·sets·O.periodic=True,·and	129	Yade·[3]:·sp.toSimulation()·············#·implicitly·sets·O.periodic=True,·and
130	O.cell.refSize·to·the·packing·period·size	130	O.cell.refSize·to·the·packing·period·size
131	Out[3]:·[4,·5,·6,·7,·8,·9,·10,·11,·12,·13,·14,·15,·16,·17,·18,·19,·20,·21~~,·22~~]	131	Out[3]:·[4,·5,·6,·7,·8,·9,·10,·11,·12,·13,·14,·15,·16,·17,·18,·19,·20,·21]

132	Yade·[4]:·O.engines+=[PeriTriaxController(goal=(-1e4,-	132	Yade·[4]:·O.engines+=[PeriTriaxController(goal=(-1e4,-
133	1e4,-.1),stressMask=0b011,maxUnbalanced=.2,doneHook='functionToRunWhenFinished	133	1e4,-.1),stressMask=0b011,maxUnbalanced=.2,doneHook='functionToRunWhenFinished
134	()')]	134	()')]
135	When·the·simulation·_\x8r_\x8u_\x8n_\x8s,·_\x8P_\x8e_\x8r_\x8i_\x8T_\x8r_\x8i_\x8a_\x8x_\x8C_\x8o_\x8n_\x8t_\x8r_\x8o_\x8l_\x8l_\x8e_\x8r·takes·over·the·control·and·calls	135	When·the·simulation·_\x8r_\x8u_\x8n_\x8s,·_\x8P_\x8e_\x8r_\x8i_\x8T_\x8r_\x8i_\x8a_\x8x_\x8C_\x8o_\x8n_\x8t_\x8r_\x8o_\x8l_\x8l_\x8e_\x8r·takes·over·the·control·and·calls
136	_\x8d_\x8o_\x8n_\x8e_\x8H_\x8o_\x8o_\x8k·when·_\x8g_\x8o_\x8a_\x8l·is·reached.·A·full·simulation·with·PeriTriaxController·might	136	_\x8d_\x8o_\x8n_\x8e_\x8H_\x8o_\x8o_\x8k·when·_\x8g_\x8o_\x8a_\x8l·is·reached.·A·full·simulation·with·PeriTriaxController·might
137	look·like·the·following:	137	look·like·the·following:


Offset 318, 15 lines modified		Offset 318, 15 lines modified
318	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8w_\x8a_\x8l_\x8l.·The·_\x8u_\x8t_\x8i_\x8l_\x8s·module·is·imported·at·startup·in·such·a·way·that·the	318	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8w_\x8a_\x8l_\x8l.·The·_\x8u_\x8t_\x8i_\x8l_\x8s·module·is·imported·at·startup·in·such·a·way·that·the
319	utils.·prefix·is·not·necessary·for·accessing·them.	319	utils.·prefix·is·not·necessary·for·accessing·them.
320	Yade·[43]:·s=sphere((0,0,0),radius=1)····#·create·sphere·particle·centered·at	320	Yade·[43]:·s=sphere((0,0,0),radius=1)····#·create·sphere·particle·centered·at
321	(0,0,0)·with·radius=1	321	(0,0,0)·with·radius=1

322	Yade·[44]:·s.shape·······················#·s.shape·describes·the·geometry·of	322	Yade·[44]:·s.shape·······················#·s.shape·describes·the·geometry·of
323	the·particle	323	the·particle
324	Out[44]:·<Sphere·instance·at·0x~~306768a~~0>	324	Out[44]:·<Sphere·instance·at·0x41147dd0>

325	Yade·[45]:·s.shape.radius················#·we·already·know·the·Sphere·class	325	Yade·[45]:·s.shape.radius················#·we·already·know·the·Sphere·class
326	Out[45]:·1.0	326	Out[45]:·1.0

327	Yade·[46]:·s.state.mass,·s.state.inertia·#·inertia·is·computed·from·density·and	327	Yade·[46]:·s.state.mass,·s.state.inertia·#·inertia·is·computed·from·density·and
328	geometry	328	geometry
329	Out[46]:	329	Out[46]:
Offset 340, 41 lines modified		Offset 340, 42 lines modified
340	In·the·last·example,·the·particle·was·fixed·in·space·by·the·fixed=True	340	In·the·last·example,·the·particle·was·fixed·in·space·by·the·fixed=True
341	parameter·to·_\x8s_\x8p_\x8h_\x8e_\x8r_\x8e;·such·a·particle·will·not·move,·creating·a·primitive	341	parameter·to·_\x8s_\x8p_\x8h_\x8e_\x8r_\x8e;·such·a·particle·will·not·move,·creating·a·primitive
342	boundary·condition.	342	boundary·condition.
343	A·particle·object·is·not·yet·part·of·the·simulation;·in·order·to·do·so,·a	343	A·particle·object·is·not·yet·part·of·the·simulation;·in·order·to·do·so,·a
344	special·function·_\x8O_\x8._\x8b_\x8o_\x8d_\x8i_\x8e_\x8s_\x8._\x8a_\x8p_\x8p_\x8e_\x8n_\x8d·(also·see·_\x8O_\x8m_\x8e_\x8g_\x8a_\x8:_\x8:_\x8b_\x8o_\x8d_\x8i_\x8e_\x8s·and·_\x8S_\x8c_\x8e_\x8n_\x8e)·is·called:	344	special·function·_\x8O_\x8._\x8b_\x8o_\x8d_\x8i_\x8e_\x8s_\x8._\x8a_\x8p_\x8p_\x8e_\x8n_\x8d·(also·see·_\x8O_\x8m_\x8e_\x8g_\x8a_\x8:_\x8:_\x8b_\x8o_\x8d_\x8i_\x8e_\x8s·and·_\x8S_\x8c_\x8e_\x8n_\x8e)·is·called:
345	Yade·[49]:·O.bodies.append(s)············#·adds·particle·s·to·the·simulation;	345	Yade·[49]:·O.bodies.append(s)············#·adds·particle·s·to·the·simulation;
346	returns·id·of·the·particle(s)·added	346	returns·id·of·the·particle(s)·added
347	Out[49]:·23	347	Out[49]:·22
348	\x8\x8\x8·P\x8Pa\x8ac\x8ck\x8ks\x8s_\x8?\x8¶·\x8\x8\x8	348	\x8\x8\x8·P\x8Pa\x8ac\x8ck\x8ks\x8s_\x8?\x8¶·\x8\x8\x8
349	There·are·functions·to·generate·a·specific·arrangement·of·particles·in·the·_\x8p_\x8a_\x8c_\x8k	349	There·are·functions·to·generate·a·specific·arrangement·of·particles·in·the·_\x8p_\x8a_\x8c_\x8k
350	module;·for·instance,·cloud·(random·loose·packing)·of·spheres·can·be·generated	350	module;·for·instance,·cloud·(random·loose·packing)·of·spheres·can·be·generated
351	with·the·_\x8p_\x8a_\x8c_\x8k_\x8._\x8S_\x8p_\x8h_\x8e_\x8r_\x8e_\x8P_\x8a_\x8c_\x8k·class:	351	with·the·_\x8p_\x8a_\x8c_\x8k_\x8._\x8S_\x8p_\x8h_\x8e_\x8r_\x8e_\x8P_\x8a_\x8c_\x8k·class:
352	Yade·[50]:·from·yade·import·pack	352	Yade·[50]:·from·yade·import·pack

353	Yade·[51]:·sp=pack.SpherePack()···················#·create·an·empty·cloud;	353	Yade·[51]:·sp=pack.SpherePack()···················#·create·an·empty·cloud;
354	SpherePack·contains·only·geometrical·information	354	SpherePack·contains·only·geometrical·information

355	Yade·[52]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.2)·#·put·spheres·with·defined	355	Yade·[52]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.2)·#·put·spheres·with·defined
356	radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)	356	radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)
357	Out[52]:·6	357	Out[52]:·7

358	Yade·[53]:·for·c,r·in·sp:·print(c,r)···············#·print·center·and·radius·of	358	Yade·[53]:·for·c,r·in·sp:·print(c,r)···············#·print·center·and·radius·of
359	all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)	359	all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)
360	···....:	360	···....:
361	Vector3(1.743361084511811931,1.632919418712122983,1.42293706056565239)·0.2
362	Vector3(1.209797575527390867,1.26915401381212356,1.611599541033277072)·0.2
363	Vector3(1.236567033580152852,1.71097494423762253,1.666367754872255524)·0.2
364	Vector3(1.785480578479552438,1.208731315909249648,1.542734237271201181)·0.2
365	Vector3(1.362079904896511318,1.504099069726329896,1.272593950254264028)·0.2
366	Vector3(1.58~~441~~329243760~~9755~~,1.5~~41999~~3~~389026~~92~~696~~,1.~~780132280~~3~~608381~~48)·0.2	361	Vector3(1.318073537322707489,1.70071306633592223,1.616667904379596843)·0.2
		362	Vector3(1.618783518329959259,1.368452960916731076,1.351716644290493541)·0.2
		363	Vector3(1.787711460873644853,1.274956656664569588,1.760851816427474903)·0.2
		364	Vector3(1.777429069017331553,1.753575335424298665,1.603234643083400357)·0.2
		365	Vector3(1.534782794051132049,1.744131292326531524,1.23427132746720436)·0.2
		366	Vector3(1.375498525279649664,1.20940091720713605,1.754099276891586179)·0.2
		367	Vector3(1.223592088423572033,1.425582912739122632,1.30683939924781134)·0.2

367	Yade·[54]:·sp.toSimulation()······················#·create·particles·and·add	368	Yade·[54]:·sp.toSimulation()······················#·create·particles·and·add
368	them·to·the·simulation	369	them·to·the·simulation
369	Out[54]:·[24,·25,·26,·27,·28,·29]	370	Out[54]:·[23,·24,·25,·26,·27,·28,·29]
370	\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8	371	\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8
371	_\x8f_\x8a_\x8c_\x8e_\x8t·(triangle·_\x8F_\x8a_\x8c_\x8e_\x8t),·_\x8w_\x8a_\x8l_\x8l·(infinite·axes-aligned·plane·_\x8W_\x8a_\x8l_\x8l)·and·_\x8b_\x8o_\x8x·(finite	372	_\x8f_\x8a_\x8c_\x8e_\x8t·(triangle·_\x8F_\x8a_\x8c_\x8e_\x8t),·_\x8w_\x8a_\x8l_\x8l·(infinite·axes-aligned·plane·_\x8W_\x8a_\x8l_\x8l)·and·_\x8b_\x8o_\x8x·(finite
372	axes-aligned·cuboids·_\x8B_\x8o_\x8x)·geometries·are·typically·used·to·define·boundaries.	373	axes-aligned·cuboids·_\x8B_\x8o_\x8x)·geometries·are·typically·used·to·define·boundaries.
373	For·instance,·a·“floor”·for·the·simulation·can·be·created·like·this:	374	For·instance,·a·“floor”·for·the·simulation·can·be·created·like·this:
374	Yade·[55]:·O.bodies.append(wall(-1,axis=2))	375	Yade·[55]:·O.bodies.append(wall(-1,axis=2))
375	Out[55]:·30	376	Out[55]:·30
376	There·are·other·convenience·functions·(like·_\x8a_\x8a_\x8b_\x8b_\x8W_\x8a_\x8l_\x8l·for·creating·closed·or	377	There·are·other·convenience·functions·(like·_\x8a_\x8a_\x8b_\x8b_\x8W_\x8a_\x8l_\x8l·for·creating·closed·or
Offset 387, 15 lines modified		Offset 388, 15 lines modified

387	Yade·[57]:·O.bodies[10].shape.radius···#·radius·of·body·#10·(will·give·error·if	388	Yade·[57]:·O.bodies[10].shape.radius···#·radius·of·body·#10·(will·give·error·if
388	not·sphere,·since·only·spheres·have·radius·defined)	389	not·sphere,·since·only·spheres·have·radius·defined)
389	Out[57]:·0.16	390	Out[57]:·0.16

390	Yade·[58]:·O.bodies[12].state.pos······#·position·of·body·#12	391	Yade·[58]:·O.bodies[12].state.pos······#·position·of·body·#12
391	Out[58]:·Vector3	392	Out[58]:·Vector3
392	(1.2~~863~~352~~9422~~5098069,1.812~~5597~~8111037~~9964~~,1.7~~77508569~~1974~~377~~16)	393	(1.727350151549889912,1.965216389871130787,1.922626001504153415)
393	Besides·that,·Yade·says·this·at·startup·(the·line·preceding·the·command-line):	394	Besides·that,·Yade·says·this·at·startup·(the·line·preceding·the·command-line):
394	[[·^L·clears·screen,·^U·kills·line.·F12·controller,·F11·3d·view,·F10·both,·F9	395	[[·^L·clears·screen,·^U·kills·line.·F12·controller,·F11·3d·view,·F10·both,·F9
395	generator,·F8·plot.·]]	396	generator,·F8·plot.·]]
396	··Controller	397	··Controller
397	······Pressing·F12·brings·up·a·window·for·controlling·the·simulation.·Although	398	······Pressing·F12·brings·up·a·window·for·controlling·the·simulation.·Although
398	······typically·no·human·intervention·is·done·in·large·simulations·(which·run	399	······typically·no·human·intervention·is·done·in·large·simulations·(which·run
399	······“headless”,·without·any·graphical·interaction),·it·can·be·handy·in·small	400	······“headless”,·without·any·graphical·interaction),·it·can·be·handy·in·small
Offset 442, 18 lines modified		Offset 443, 18 lines modified
442	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#	443	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#
443	define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily	444	define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily
444	···....:·]	445	···....:·]
445	···....:	446	···....:

446	Yade·[61]:·O.engines	447	Yade·[61]:·O.engines
447	Out[61]:	448	Out[61]:
448	[<ForceResetter·instance·at·0x~~305e5ff~~0>,	449	[<ForceResetter·instance·at·0x41119970>,
449	·<InsertionSortCollider·instance·at·0x30~~63f2~~70>,	450	·<InsertionSortCollider·instance·at·0x40fdea70>,
450	·<InteractionLoop·instance·at·0x~~304b3a0~~0>,	451	·<InteractionLoop·instance·at·0x41034de0>,
451	·<NewtonIntegrator·instance·at·0x306b4510>]	452	·<NewtonIntegrator·instance·at·0x4109bed0>]

452	Yade·[62]:·O.engines[-1]==newtonCustomLabel····#·is·it·the·same·object?	453	Yade·[62]:·O.engines[-1]==newtonCustomLabel····#·is·it·the·same·object?
453	Out[62]:·True	454	Out[62]:·True

454	Yade·[63]:·newtonCustomLabel.damping	455	Yade·[63]:·newtonCustomLabel.damping
455	Out[63]:·0.2	456	Out[63]:·0.2
456	Instead·of·typing·everything·into·the·command-line,·one·can·describe·simulation	457	Instead·of·typing·everything·into·the·command-line,·one·can·describe·simulation


Offset 132, 15 lines modified		Offset 132, 15 lines modified
132	module;·to·mention·a·few·of·them,·they·are·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8s_\x8p_\x8h_\x8e_\x8r_\x8e,·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8f_\x8a_\x8c_\x8e_\x8t,	132	module;·to·mention·a·few·of·them,·they·are·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8s_\x8p_\x8h_\x8e_\x8r_\x8e,·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8f_\x8a_\x8c_\x8e_\x8t,
133	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8w_\x8a_\x8l_\x8l.	133	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8w_\x8a_\x8l_\x8l.
134	Yade·[8]:·s=utils.sphere((0,0,0),radius=1)····#·create·sphere·particle·centered	134	Yade·[8]:·s=utils.sphere((0,0,0),radius=1)····#·create·sphere·particle·centered
135	at·(0,0,0)·with·radius=1	135	at·(0,0,0)·with·radius=1

136	Yade·[9]:·s.shape·······················#·s.shape·describes·the·geometry·of·the	136	Yade·[9]:·s.shape·······················#·s.shape·describes·the·geometry·of·the
137	particle	137	particle
138	Out[9]:·<Sphere·instance·at·0x~~3070083~~0>	138	Out[9]:·<Sphere·instance·at·0x41147e70>

139	Yade·[10]:·s.shape.radius················#·we·already·know·the·Sphere·class	139	Yade·[10]:·s.shape.radius················#·we·already·know·the·Sphere·class
140	Out[10]:·1.0	140	Out[10]:·1.0

141	Yade·[11]:·s.state.mass,·s.state.inertia·#·inertia·is·computed·from·density·and	141	Yade·[11]:·s.state.mass,·s.state.inertia·#·inertia·is·computed·from·density·and
142	geometry	142	geometry
143	Out[11]:	143	Out[11]:
Offset 167, 57 lines modified		Offset 167, 59 lines modified
167	Yade·[15]:·from·yade·import·pack	167	Yade·[15]:·from·yade·import·pack

168	Yade·[16]:·sp=pack.SpherePack()···················#·create·an·empty·cloud;	168	Yade·[16]:·sp=pack.SpherePack()···················#·create·an·empty·cloud;
169	SpherePack·contains·only·geometrical·information	169	SpherePack·contains·only·geometrical·information

170	Yade·[17]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.2)·#·put·spheres·with·defined	170	Yade·[17]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.2)·#·put·spheres·with·defined
171	radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)	171	radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)
172	Out[17]:·7	172	Out[17]:·9

173	Yade·[18]:·for·c,r·in·sp:·print(c,r)···············#·print·center·and·radius·of	173	Yade·[18]:·for·c,r·in·sp:·print(c,r)···············#·print·center·and·radius·of
174	all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)	174	all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)
175	···....:	175	···....:
176	Vector3(1.381656144299515443,1.291893403155796927,1.507360149671662874)·0.2
177	Vector3(1.485388405672678935,1.73779686837323788,1.521650382584594174)·0.2
178	Vector3(1.764107768509895369,1.39377750251065935,1.204539647455342699)·0.2
179	Vector3(1.702849456059038591,1.44549468982342888,1.708449508360432967)·0.2
180	Vector3(1.213644163187294289,1.673636578379339435,1.230104533601957817)·0.2
181	Vector3(1.209697637290100047,1.533678182210546082,1.784571461152755001)·0.2
182	Vector3(1.~~775~~92~~79321~~55~~509~~925,1.~~7968~~403685453~~0893~~,1.20~~2872~~510~~620~~43854)·0.2	176	Vector3(1.522901880554619058,1.552211411648142914,1.505146590952437524)·0.2
		177	Vector3(1.423201801633421137,1.24116767288482599,1.792068191667541832)·0.2
		178	Vector3(1.244714985720335898,1.390535278559828614,1.240790309984063366)·0.2
		179	Vector3(1.217144275936492104,1.732549160894300222,1.71567609868495774)·0.2
		180	Vector3(1.615646009895546964,1.228810015880396289,1.267525650674329096)·0.2
		181	Vector3(1.289830296061500903,1.792343648841321357,1.278823455046943502)·0.2
		182	Vector3(1.78542611114205152,1.761482662691111312,1.24715423964827532)·0.2
		183	Vector3(1.79751660300491567,1.22880671145319198,1.648653591264860996)·0.2
		184	Vector3(1.742037138998754564,1.771296988874261125,1.762201438661530561)·0.2

183	Yade·[19]:·sp.toSimulation()······················#·create·particles·and·add	185	Yade·[19]:·sp.toSimulation()······················#·create·particles·and·add
184	them·to·the·simulation	186	them·to·the·simulation
185	Out[19]:·[1,·2,·3,·4,·5,·6,·7]	187	Out[19]:·[1,·2,·3,·4,·5,·6,·7,·8,·9]
186	\x8\x8\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8\x8\x8	188	\x8\x8\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8\x8\x8
187	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8f_\x8a_\x8c_\x8e_\x8t·(triangle·_\x8F_\x8a_\x8c_\x8e_\x8t)·and·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8w_\x8a_\x8l_\x8l·(infinite·axes-aligned·plane·_\x8W_\x8a_\x8l_\x8l)	189	_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8f_\x8a_\x8c_\x8e_\x8t·(triangle·_\x8F_\x8a_\x8c_\x8e_\x8t)·and·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8w_\x8a_\x8l_\x8l·(infinite·axes-aligned·plane·_\x8W_\x8a_\x8l_\x8l)
188	geometries·are·typically·used·to·define·boundaries.·For·instance,·a·“floor”·for	190	geometries·are·typically·used·to·define·boundaries.·For·instance,·a·“floor”·for
189	the·simulation·can·be·created·like·this:	191	the·simulation·can·be·created·like·this:
190	Yade·[20]:·O.bodies.append(utils.wall(-1,axis=2))	192	Yade·[20]:·O.bodies.append(utils.wall(-1,axis=2))
191	Out[20]:·8	193	Out[20]:·10
192	There·are·other·conveinence·functions·(like·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8f_\x8a_\x8c_\x8e_\x8t_\x8B_\x8o_\x8x·for·creating·closed	194	There·are·other·conveinence·functions·(like·_\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8f_\x8a_\x8c_\x8e_\x8t_\x8B_\x8o_\x8x·for·creating·closed
193	or·open·rectangular·box,·or·family·of·_\x8y_\x8m_\x8p_\x8o_\x8r_\x8t·functions)	195	or·open·rectangular·box,·or·family·of·_\x8y_\x8m_\x8p_\x8o_\x8r_\x8t·functions)
194	\x8\x8\x8\x8\x8·L\x8Lo\x8oo\x8ok\x8k·i\x8in\x8ns\x8si\x8id\x8de\x8e_\x8?\x8¶·\x8\x8\x8\x8\x8	196	\x8\x8\x8\x8\x8·L\x8Lo\x8oo\x8ok\x8k·i\x8in\x8ns\x8si\x8id\x8de\x8e_\x8?\x8¶·\x8\x8\x8\x8\x8
195	The·simulation·can·be·inspected·in·several·ways.·All·data·can·be·accessed·from	197	The·simulation·can·be·inspected·in·several·ways.·All·data·can·be·accessed·from
196	python·directly:	198	python·directly:
197	Yade·[21]:·len(O.bodies)	199	Yade·[21]:·len(O.bodies)
198	Out[21]:·9	200	Out[21]:·11

199	Yade·[22]:·O.bodies[10].shape.radius···#·radius·of·body·#10·(will·give·error·if	201	Yade·[22]:·O.bodies[10].shape.radius···#·radius·of·body·#10·(will·give·error·if
200	not·sphere,·since·only·spheres·have·radius·defined)	202	not·sphere,·since·only·spheres·have·radius·defined)
201	[0;31m-------------------------------------------------------------------------	203	[0;31m-------------------------------------------------------------------------
202	--\x1b[0m	204	--\x1b[0m
203	[0;31m~~Index~~Error.[0m~~····~~····························Traceback·(most·recent·call	205	[0;31mAttributeError.[0m····························Traceback·(most·recent·call
204	last)	206	last)
205	Cell·\x1b[0;32mIn[22],·line·1\x1b[0m	207	Cell·\x1b[0;32mIn[22],·line·1\x1b[0m
206	[0;32m---->·1\x1b[0m·\x1b[43mO\x1b[49m\x1b[38;5;241;43m.\x1b[39;49m\x1b[43mbodies\x1b[49m\x1b[43m[\x1b	208	[0;32m---->·1\x1b[0m·\x1b[43mO\x1b[49m\x1b[38;5;241;43m.\x1b[39;49m\x1b[43mbodies\x1b[49m\x1b[43m[\x1b
207	[49m\x1b[38;5;241;43m10\x1b[39;49m\x1b[43m]\x1b[49m\x1b[38;5;241m..[39mshape.[~~38;5;2~~41m.\x1b	209	[49m\x1b[38;5;241;43m10\x1b[39;49m\x1b[43m]\x1b[49m\x1b[38;5;241;43m..[39;49m.[43mshape.[49m\x1b
208	[39mradius···\x1b[38;5;66;03m#·radius·of·body·#10·(will·give·error·if·not·sphere,
209	~~since·only·spheres·have·~~radius·~~defined)~~.[39;00m	210	[38;5;241;43m..[39;49m.[43mradius.[49m···.[38;5;66;03m#·radius·of·body·#10
		211	(will·give·error·if·not·sphere,·since·only·spheres·have·radius·defined)\x1b[39;00m

210	[0;31m~~Index~~Error.[0m:·Body·id·out~~·of~~·ra~~nge.~~	212	[0;31mAttributeError.[0m:·'Wall'·object·has·no·attribute·'radius'

211	Yade·[23]:·O.bodies[12].state.pos······#·position·of·body·#12	213	Yade·[23]:·O.bodies[12].state.pos······#·position·of·body·#12
212	[0;31m-------------------------------------------------------------------------	214	[0;31m-------------------------------------------------------------------------
213	--\x1b[0m	215	--\x1b[0m
214	[0;31mIndexError\x1b[0m································Traceback·(most·recent·call	216	[0;31mIndexError\x1b[0m································Traceback·(most·recent·call
215	last)	217	last)
216	Cell·\x1b[0;32mIn[23],·line·1\x1b[0m	218	Cell·\x1b[0;32mIn[23],·line·1\x1b[0m
Offset 263, 18 lines modified		Offset 265, 18 lines modified
263	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#	265	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#
264	define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily	266	define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily
265	···....:·]	267	···....:·]
266	···....:	268	···....:

267	Yade·[25]:·O.engines	269	Yade·[25]:·O.engines
268	Out[25]:	270	Out[25]:
269	[<ForceResetter·instance·at·0x~~30910e3~~0>,	271	[<ForceResetter·instance·at·0x4136a000>,
270	·<InsertionSortCollider·instance·at·0x~~308dc1~~60>,	272	·<InsertionSortCollider·instance·at·0x4134f460>,
271	·<InteractionLoop·instance·at·0x~~308e466~~0>,	273	·<InteractionLoop·instance·at·0x4132c900>,
272	·<NewtonIntegrator·instance·at·0x30~~6634b~~0>]	274	·<NewtonIntegrator·instance·at·0x405f1d50>]

273	Yade·[26]:·O.engines[-1]==newtonCustomLabel····#·is·it·the·same·object?	275	Yade·[26]:·O.engines[-1]==newtonCustomLabel····#·is·it·the·same·object?
274	Out[26]:·True	276	Out[26]:·True

275	Yade·[27]:·newtonCustomLabel.damping	277	Yade·[27]:·newtonCustomLabel.damping
276	Out[27]:·0.2	278	Out[27]:·0.2
277	Instead·of·typing·everything·into·the·command-line,·one·can·describe·simulation	279	Instead·of·typing·everything·into·the·command-line,·one·can·describe·simulation


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54	-rw-r--r--···0·root·········(0)·root·········(0)·····~~4780~~·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-~~1bee2c390~~cb5df1~~da829~~c7~~1deb~~4~~b4d9~~d~~b127a~~639.png.map	62	-rw-r--r--···0·root·········(0)·root·········(0)·····2093·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-367b8a629c7c10ef40c6f2f4f390d7f6006ce89e.png.map
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356	</div>	356	</div>
357	<p>Normal·simulations,·however,·are·run·continuously.·Starting/stopping·the·loop·is·done·by·<code·class="docutils·literal·notranslate"><span·class="pre">O.run()</span></code>·and·<code·class="docutils·literal·notranslate"><span·class="pre">O.pause()</span></code>;·note·that·<code·class="docutils·literal·notranslate"><span·class="pre">O.run()</span></code>·returns·control·to·Python·and·the·simulation·runs·in·background;·if·you·want·to·wait·for·it·to·finish,·use·<code·class="docutils·literal·notranslate"><span·class="pre">O.wait()</span></code>.·Fixed·number·of·steps·can·be·run·with·<code·class="docutils·literal·notranslate"><span·class="pre">O.run(1000)</span></code>,·<code·class="docutils·literal·notranslate"><span·class="pre">O.run(1000,True)</span></code>·will·run·and·wait.·To·stop·at·absolute·step·number,·<code·class="docutils·literal·notranslate"><span·class="pre">O.stopAtIter</span></code>·can·be·set·and·<code·class="docutils·literal·notranslate"><span·class="pre">O.run()</span></code>·called·normally.</p>	357	<p>Normal·simulations,·however,·are·run·continuously.·Starting/stopping·the·loop·is·done·by·<code·class="docutils·literal·notranslate"><span·class="pre">O.run()</span></code>·and·<code·class="docutils·literal·notranslate"><span·class="pre">O.pause()</span></code>;·note·that·<code·class="docutils·literal·notranslate"><span·class="pre">O.run()</span></code>·returns·control·to·Python·and·the·simulation·runs·in·background;·if·you·want·to·wait·for·it·to·finish,·use·<code·class="docutils·literal·notranslate"><span·class="pre">O.wait()</span></code>.·Fixed·number·of·steps·can·be·run·with·<code·class="docutils·literal·notranslate"><span·class="pre">O.run(1000)</span></code>,·<code·class="docutils·literal·notranslate"><span·class="pre">O.run(1000,True)</span></code>·will·run·and·wait.·To·stop·at·absolute·step·number,·<code·class="docutils·literal·notranslate"><span·class="pre">O.stopAtIter</span></code>·can·be·set·and·<code·class="docutils·literal·notranslate"><span·class="pre">O.run()</span></code>·called·normally.</p>
358	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[12]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">run</span><span·class="p">()</span>	358	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[12]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">run</span><span·class="p">()</span>

359	<span·class="gp">Yade·[13]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">pause</span><span·class="p">()</span>	359	<span·class="gp">Yade·[13]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">pause</span><span·class="p">()</span>

360	<span·class="gp">Yade·[14]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">iter</span>	360	<span·class="gp">Yade·[14]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">iter</span>
361	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">14</span><span·class="p">]:</span>·<span·class="mi">~~558~~</span>	361	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">14</span><span·class="p">]:</span>·<span·class="mi">723</span>

362	<span·class="gp">Yade·[15]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">run</span><span·class="p">(</span><span·class="mi">100000</span><span·class="p">,</span><span·class="kc">True</span><span·class="p">)</span>	362	<span·class="gp">Yade·[15]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">run</span><span·class="p">(</span><span·class="mi">100000</span><span·class="p">,</span><span·class="kc">True</span><span·class="p">)</span>

363	<span·class="gp">Yade·[16]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">iter</span>	363	<span·class="gp">Yade·[16]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">iter</span>
364	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">16</span><span·class="p">]:</span>·<span·class="mi">100~~558~~</span>	364	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">16</span><span·class="p">]:</span>·<span·class="mi">100723</span>

365	<span·class="gp">Yade·[17]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">stopAtIter</span><span·class="o">=</span><span·class="mi">500000</span>	365	<span·class="gp">Yade·[17]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">stopAtIter</span><span·class="o">=</span><span·class="mi">500000</span>

366	<span·class="gp">Yade·[18]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">run</span><span·class="p">()</span>	366	<span·class="gp">Yade·[18]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">run</span><span·class="p">()</span>

367	<span·class="gp">Yade·[19]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">wait</span><span·class="p">()</span>	367	<span·class="gp">Yade·[19]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">wait</span><span·class="p">()</span>

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433	<h2>Architecture·overview<a·class="headerlink"·href="#architecture-overview"·title="Link·to·this·heading">¶</a></h2>	433	<h2>Architecture·overview<a·class="headerlink"·href="#architecture-overview"·title="Link·to·this·heading">¶</a></h2>
434	<p>In·the·following,·a·high-level·overview·of·Yade·architecture·will·be·given.·As·many·of·the·features·are·directly·represented·in·simulation·scripts,·which·are·written·in·Python,·being·familiar·with·this·language·will·help·you·follow·the·examples.·For·the·rest,·this·knowledge·is·not·strictly·necessary·and·you·can·ignore·code·examples.</p>	434	<p>In·the·following,·a·high-level·overview·of·Yade·architecture·will·be·given.·As·many·of·the·features·are·directly·represented·in·simulation·scripts,·which·are·written·in·Python,·being·familiar·with·this·language·will·help·you·follow·the·examples.·For·the·rest,·this·knowledge·is·not·strictly·necessary·and·you·can·ignore·code·examples.</p>
435	<section·id="data-and-functions">	435	<section·id="data-and-functions">
436	<h3>Data·and·functions<a·class="headerlink"·href="#data-and-functions"·title="Link·to·this·heading">¶</a></h3>	436	<h3>Data·and·functions<a·class="headerlink"·href="#data-and-functions"·title="Link·to·this·heading">¶</a></h3>
437	<p>To·assure·flexibility·of·software·design,·yade·makes·clear·distinction·of·2·families·of·classes:·<em>data</em>·components·and·<em>functional</em>·components.·The·former·only·store·data·without·providing·functionality,·while·the·latter·define·functions·operating·on·the·data.·In·programming,·this·is·known·as·<em>visitor</em>·pattern·(as·functional·components·“visit”·the·data,·without·being·bound·to·them·explicitly).</p>	437	<p>To·assure·flexibility·of·software·design,·yade·makes·clear·distinction·of·2·families·of·classes:·<em>data</em>·components·and·<em>functional</em>·components.·The·former·only·store·data·without·providing·functionality,·while·the·latter·define·functions·operating·on·the·data.·In·programming,·this·is·known·as·<em>visitor</em>·pattern·(as·functional·components·“visit”·the·data,·without·being·bound·to·them·explicitly).</p>
438	<p>Entire·simulation,·i.e.·both·data·and·functions,·are·stored·in·a·single·<code·class="docutils·literal·notranslate"><span·class="pre">Scene</span></code>·object.·It·is·accessible·through·the·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega">Omega</a>·class·in·python·(a·singleton),·which·is·by·default·stored·in·the·<code·class="docutils·literal·notranslate"><span·class="pre">O</span></code>·global·variable:</p>	438	<p>Entire·simulation,·i.e.·both·data·and·functions,·are·stored·in·a·single·<code·class="docutils·literal·notranslate"><span·class="pre">Scene</span></code>·object.·It·is·accessible·through·the·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega">Omega</a>·class·in·python·(a·singleton),·which·is·by·default·stored·in·the·<code·class="docutils·literal·notranslate"><span·class="pre">O</span></code>·global·variable:</p>
439	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[28]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">bodies</span>·······<span·class="c1">#·some·data·components</span>	439	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[28]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">bodies</span>·······<span·class="c1">#·some·data·components</span>
440	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">28</span><span·class="p">]:</span>·<span·class="o"><</span><span·class="n">yade</span><span·class="o">.</span><span·class="n">wrapper</span><span·class="o">.</span><span·class="n">BodyContainer</span>·<span·class="n">at</span>·<span·class="mh">0xffff~~643~~1fa00</span><span·class="o">></span>	440	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">28</span><span·class="p">]:</span>·<span·class="o"><</span><span·class="n">yade</span><span·class="o">.</span><span·class="n">wrapper</span><span·class="o">.</span><span·class="n">BodyContainer</span>·<span·class="n">at</span>·<span·class="mh">0xffff55f1fa70</span><span·class="o">></span>

441	<span·class="gp">Yade·[29]:·</span><span·class="nb">len</span><span·class="p">(</span><span·class="n">O</span><span·class="o">.</span><span·class="n">bodies</span><span·class="p">)</span>··<span·class="c1">#·there·are·no·bodies·as·of·yet</span>	441	<span·class="gp">Yade·[29]:·</span><span·class="nb">len</span><span·class="p">(</span><span·class="n">O</span><span·class="o">.</span><span·class="n">bodies</span><span·class="p">)</span>··<span·class="c1">#·there·are·no·bodies·as·of·yet</span>
442	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">29</span><span·class="p">]:</span>·<span·class="mi">0</span>	442	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">29</span><span·class="p">]:</span>·<span·class="mi">0</span>

443	<span·class="gp">Yade·[30]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span>······<span·class="c1">#·functional·components,·empty·at·the·moment</span>	443	<span·class="gp">Yade·[30]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span>······<span·class="c1">#·functional·components,·empty·at·the·moment</span>
444	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">30</span><span·class="p">]:</span>·<span·class="p">[]</span>	444	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">30</span><span·class="p">]:</span>·<span·class="p">[]</span>
445	</pre></div>	445	</pre></div>
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472	</figure>	472	</figure>


Offset 1249, 19 lines modified		Offset 1249, 19 lines modified
1249	<span·class="w">»»</span><span·class="nt"><trackEnergy></span>0<span·class="nt"></trackEnergy></span>	1249	<span·class="w">»»</span><span·class="nt"><trackEnergy></span>0<span·class="nt"></trackEnergy></span>
1250	<span·class="w">»»</span><span·class="nt"><doSort></span>0<span·class="nt"></doSort></span>	1250	<span·class="w">»»</span><span·class="nt"><doSort></span>0<span·class="nt"></doSort></span>
1251	<span·class="w">»»</span><span·class="nt"><runInternalConsistencyChecks></span>1<span·class="nt"></runInternalConsistencyChecks></span>	1251	<span·class="w">»»</span><span·class="nt"><runInternalConsistencyChecks></span>1<span·class="nt"></runInternalConsistencyChecks></span>
1252	<span·class="w">»»</span><span·class="nt"><selectedBody></span>-1<span·class="nt"></selectedBody></span>	1252	<span·class="w">»»</span><span·class="nt"><selectedBody></span>-1<span·class="nt"></selectedBody></span>
1253	<span·class="w">»»</span><span·class="nt"><tags</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"3"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="nt">></span>	1253	<span·class="w">»»</span><span·class="nt"><tags</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"3"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="nt">></span>
1254	<span·class="w">»»»</span><span·class="nt"><count></span>5<span·class="nt"></count></span>	1254	<span·class="w">»»»</span><span·class="nt"><count></span>5<span·class="nt"></count></span>
1255	<span·class="w">»»»</span><span·class="nt"><item_version></span>0<span·class="nt"></item_version></span>	1255	<span·class="w">»»»</span><span·class="nt"><item_version></span>0<span·class="nt"></item_version></span>
1256	<span·class="w">»»»</span><span·class="nt"><item></span>author=~(pbuilder1@codeth~~ink04-ar~~m64)<span·class="nt"></item></span>	1256	<span·class="w">»»»</span><span·class="nt"><item></span>author=second~user~(pbuilder2@i-capture-the-hostname)<span·class="nt"></item></span>
1257	<span·class="w">»»»</span><span·class="nt"><item></span>isoTime=20250~~727~~T~~113446~~<span·class="nt"></item></span>	1257	<span·class="w">»»»</span><span·class="nt"><item></span>isoTime=20260831T035003<span·class="nt"></item></span>
1258	<span·class="w">»»»</span><span·class="nt"><item></span>id=20250~~727~~T~~113446~~p32~~57836~~<span·class="nt"></item></span>	1258	<span·class="w">»»»</span><span·class="nt"><item></span>id=20260831T035003p363122<span·class="nt"></item></span>
1259	<span·class="w">»»»</span><span·class="nt"><item></span>d.id=20250~~727~~T~~113446~~p32~~57836~~<span·class="nt"></item></span>	1259	<span·class="w">»»»</span><span·class="nt"><item></span>d.id=20260831T035003p363122<span·class="nt"></item></span>
1260	<span·class="w">»»»</span><span·class="nt"><item></span>id.d=20250~~727~~T~~113446~~p32~~57836~~<span·class="nt"></item></span>	1260	<span·class="w">»»»</span><span·class="nt"><item></span>id.d=20260831T035003p363122<span·class="nt"></item></span>
1261	<span·class="w">»»</span><span·class="nt"></tags></span>	1261	<span·class="w">»»</span><span·class="nt"></tags></span>
1262	<span·class="w">»»</span><span·class="nt"><engines</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"4"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="nt">></span>	1262	<span·class="w">»»</span><span·class="nt"><engines</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"4"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="nt">></span>
1263	<span·class="w">»»»</span><span·class="nt"><count></span>1<span·class="nt"></count></span>	1263	<span·class="w">»»»</span><span·class="nt"><count></span>1<span·class="nt"></count></span>
1264	<span·class="w">»»»</span><span·class="nt"><item_version></span>1<span·class="nt"></item_version></span>	1264	<span·class="w">»»»</span><span·class="nt"><item_version></span>1<span·class="nt"></item_version></span>
1265	<span·class="w">»»»</span><span·class="nt"><item</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"5"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"1"</span><span·class="nt">></span>	1265	<span·class="w">»»»</span><span·class="nt"><item</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"5"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"1"</span><span·class="nt">></span>
1266	<span·class="w">»»»»</span><span·class="nt"><px</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"7"</span><span·class="w">·</span><span·class="na">class_name=</span><span·class="s">"yade::GravityEngine"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"1"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">object_id=</span><span·class="s">"_2"</span><span·class="nt">></span>	1266	<span·class="w">»»»»</span><span·class="nt"><px</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"7"</span><span·class="w">·</span><span·class="na">class_name=</span><span·class="s">"yade::GravityEngine"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"1"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">object_id=</span><span·class="s">"_2"</span><span·class="nt">></span>
1267	<span·class="w">»»»»»</span><span·class="nt"><FieldApplier</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"8"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"1"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">object_id=</span><span·class="s">"_3"</span><span·class="nt">></span>	1267	<span·class="w">»»»»»</span><span·class="nt"><FieldApplier</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"8"</span><span·class="w">·</span><span·class="na">tracking_level=</span><span·class="s">"1"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"0"</span><span·class="w">·</span><span·class="na">object_id=</span><span·class="s">"_3"</span><span·class="nt">></span>
Offset 1926, 15 lines modified		Offset 1926, 15 lines modified
1926	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[42]:·</span><span·class="n">ld</span><span·class="o">=</span><span·class="n">LawDispatcher</span><span·class="p">([</span><span·class="n">Law2_ScGeom_CpmPhys_Cpm</span><span·class="p">()])</span>	1926	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[42]:·</span><span·class="n">ld</span><span·class="o">=</span><span·class="n">LawDispatcher</span><span·class="p">([</span><span·class="n">Law2_ScGeom_CpmPhys_Cpm</span><span·class="p">()])</span>

1927	<span·class="gp">Yade·[43]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>	1927	<span·class="gp">Yade·[43]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>
1928	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">43</span><span·class="p">]:</span>·<span·class="p">{(</span><span·class="s1">'GenericSpheresContact'</span><span·class="p">,</span>·<span·class="s1">'CpmPhys'</span><span·class="p">):</span>·<span·class="s1">'Law2_ScGeom_CpmPhys_Cpm'</span><span·class="p">}</span>	1928	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">43</span><span·class="p">]:</span>·<span·class="p">{(</span><span·class="s1">'GenericSpheresContact'</span><span·class="p">,</span>·<span·class="s1">'CpmPhys'</span><span·class="p">):</span>·<span·class="s1">'Law2_ScGeom_CpmPhys_Cpm'</span><span·class="p">}</span>

1929	<span·class="c">#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request</span>	1929	<span·class="c">#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request</span>
1930	<span·class="gp">Yade·[44]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispFunctor</span><span·class="p">(</span><span·class="n">ScGridCoGeom</span><span·class="p">(),</span><span·class="n">CpmPhys</span><span·class="p">())</span>	1930	<span·class="gp">Yade·[44]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispFunctor</span><span·class="p">(</span><span·class="n">ScGridCoGeom</span><span·class="p">(),</span><span·class="n">CpmPhys</span><span·class="p">())</span>
1931	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">44</span><span·class="p">]:</span>·<span·class="o"><</span><span·class="n">Law2_ScGeom_CpmPhys_Cpm</span>·<span·class="n">instance</span>·<span·class="n">at</span>·<span·class="mh">0x30~~56e62~~0</span><span·class="o">></span>	1931	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">44</span><span·class="p">]:</span>·<span·class="o"><</span><span·class="n">Law2_ScGeom_CpmPhys_Cpm</span>·<span·class="n">instance</span>·<span·class="n">at</span>·<span·class="mh">0x40fb2240</span><span·class="o">></span>

1932	<span·class="gp">Yade·[45]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>	1932	<span·class="gp">Yade·[45]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>
1933	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">45</span><span·class="p">]:</span>·	1933	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">45</span><span·class="p">]:</span>·
1934	<span·class="go">{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',</span>	1934	<span·class="go">{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',</span>
1935	<span·class="go">·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}</span>	1935	<span·class="go">·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}</span>
1936	</pre></div>	1936	</pre></div>
1937	</div>	1937	</div>
Offset 2054, 27 lines modified		Offset 2054, 27 lines modified
2054	<span·class="gp">Yade·[51]:·</span><span·class="n">yade</span><span·class="o">.</span><span·class="n">timing</span><span·class="o">.</span><span·class="n">reset</span><span·class="p">()</span>···················<span·class="c1">##·not·necessary·if·used·for·the·first·time</span>	2054	<span·class="gp">Yade·[51]:·</span><span·class="n">yade</span><span·class="o">.</span><span·class="n">timing</span><span·class="o">.</span><span·class="n">reset</span><span·class="p">()</span>···················<span·class="c1">##·not·necessary·if·used·for·the·first·time</span>


Offset 469, 15 lines modified		Offset 469, 15 lines modified
469	<li><p>Set·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Body.material">Body.material</a>·(last-defined·material·is·used,·otherwise·a·default·material·is·created)</p></li>	469	<li><p>Set·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Body.material">Body.material</a>·(last-defined·material·is·used,·otherwise·a·default·material·is·created)</p></li>
470	<li><p>Set·position·and·orientation·in·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Body.state">Body.state</a>,·compute·mass·and·moment·of·inertia·based·on·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Material">Material</a>·and·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Shape">Shape</a></p></li>	470	<li><p>Set·position·and·orientation·in·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Body.state">Body.state</a>,·compute·mass·and·moment·of·inertia·based·on·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Material">Material</a>·and·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Shape">Shape</a></p></li>
471	</ol>	471	</ol>
472	<p>In·order·to·avoid·such·tasks,·shorthand·functions·are·defined·in·the·<a·class="reference·external"·href="yade.utils.html#">utils</a>·module;·to·mention·a·few·of·them,·they·are·<a·class="reference·external"·href="yade.utils.html#yade.utils.sphere">utils.sphere</a>,·<a·class="reference·external"·href="yade.utils.html#yade.utils.facet">utils.facet</a>,·<a·class="reference·external"·href="yade.utils.html#yade.utils.wall">utils.wall</a>.·The·<a·class="reference·external"·href="yade.utils.html#">utils</a>·module·is·imported·at·startup·in·such·a·way·that·the·<code·class="docutils·literal·notranslate"><span·class="pre">utils.</span></code>·prefix·is·not·necessary·for·accessing·them.</p>	472	<p>In·order·to·avoid·such·tasks,·shorthand·functions·are·defined·in·the·<a·class="reference·external"·href="yade.utils.html#">utils</a>·module;·to·mention·a·few·of·them,·they·are·<a·class="reference·external"·href="yade.utils.html#yade.utils.sphere">utils.sphere</a>,·<a·class="reference·external"·href="yade.utils.html#yade.utils.facet">utils.facet</a>,·<a·class="reference·external"·href="yade.utils.html#yade.utils.wall">utils.wall</a>.·The·<a·class="reference·external"·href="yade.utils.html#">utils</a>·module·is·imported·at·startup·in·such·a·way·that·the·<code·class="docutils·literal·notranslate"><span·class="pre">utils.</span></code>·prefix·is·not·necessary·for·accessing·them.</p>
473	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[43]:·</span><span·class="n">s</span><span·class="o">=</span><span·class="n">sphere</span><span·class="p">((</span><span·class="mi">0</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">),</span><span·class="n">radius</span><span·class="o">=</span><span·class="mi">1</span><span·class="p">)</span>····<span·class="c1">#·create·sphere·particle·centered·at·(0,0,0)·with·radius=1</span>	473	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[43]:·</span><span·class="n">s</span><span·class="o">=</span><span·class="n">sphere</span><span·class="p">((</span><span·class="mi">0</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">),</span><span·class="n">radius</span><span·class="o">=</span><span·class="mi">1</span><span·class="p">)</span>····<span·class="c1">#·create·sphere·particle·centered·at·(0,0,0)·with·radius=1</span>

474	<span·class="gp">Yade·[44]:·</span><span·class="n">s</span><span·class="o">.</span><span·class="n">shape</span>·······················<span·class="c1">#·s.shape·describes·the·geometry·of·the·particle</span>	474	<span·class="gp">Yade·[44]:·</span><span·class="n">s</span><span·class="o">.</span><span·class="n">shape</span>·······················<span·class="c1">#·s.shape·describes·the·geometry·of·the·particle</span>
475	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">44</span><span·class="p">]:</span>·<span·class="o"><</span><span·class="n">Sphere</span>·<span·class="n">instance</span>·<span·class="n">at</span>·<span·class="mh">0x~~306768a~~0</span><span·class="o">></span>	475	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">44</span><span·class="p">]:</span>·<span·class="o"><</span><span·class="n">Sphere</span>·<span·class="n">instance</span>·<span·class="n">at</span>·<span·class="mh">0x41147dd0</span><span·class="o">></span>

476	<span·class="gp">Yade·[45]:·</span><span·class="n">s</span><span·class="o">.</span><span·class="n">shape</span><span·class="o">.</span><span·class="n">radius</span>················<span·class="c1">#·we·already·know·the·Sphere·class</span>	476	<span·class="gp">Yade·[45]:·</span><span·class="n">s</span><span·class="o">.</span><span·class="n">shape</span><span·class="o">.</span><span·class="n">radius</span>················<span·class="c1">#·we·already·know·the·Sphere·class</span>
477	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">45</span><span·class="p">]:</span>·<span·class="mf">1.0</span>	477	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">45</span><span·class="p">]:</span>·<span·class="mf">1.0</span>

478	<span·class="gp">Yade·[46]:·</span><span·class="n">s</span><span·class="o">.</span><span·class="n">state</span><span·class="o">.</span><span·class="n">mass</span><span·class="p">,</span>·<span·class="n">s</span><span·class="o">.</span><span·class="n">state</span><span·class="o">.</span><span·class="n">inertia</span>·<span·class="c1">#·inertia·is·computed·from·density·and·geometry</span>	478	<span·class="gp">Yade·[46]:·</span><span·class="n">s</span><span·class="o">.</span><span·class="n">state</span><span·class="o">.</span><span·class="n">mass</span><span·class="p">,</span>·<span·class="n">s</span><span·class="o">.</span><span·class="n">state</span><span·class="o">.</span><span·class="n">inertia</span>·<span·class="c1">#·inertia·is·computed·from·density·and·geometry</span>
479	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">46</span><span·class="p">]:</span>·	479	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">46</span><span·class="p">]:</span>·
480	<span·class="go">(4188.790204786391,</span>	480	<span·class="go">(4188.790204786391,</span>
Offset 488, 39 lines modified		Offset 488, 40 lines modified

488	<span·class="gp">Yade·[48]:·</span><span·class="n">s2</span><span·class="o">=</span><span·class="n">sphere</span><span·class="p">((</span><span·class="o">-</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">),</span><span·class="n">radius</span><span·class="o">=</span><span·class="mi">1</span><span·class="p">,</span><span·class="n">fixed</span><span·class="o">=</span><span·class="kc">True</span><span·class="p">)</span>·····<span·class="c1">#·explanation·below</span>	488	<span·class="gp">Yade·[48]:·</span><span·class="n">s2</span><span·class="o">=</span><span·class="n">sphere</span><span·class="p">((</span><span·class="o">-</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">,</span><span·class="mi">0</span><span·class="p">),</span><span·class="n">radius</span><span·class="o">=</span><span·class="mi">1</span><span·class="p">,</span><span·class="n">fixed</span><span·class="o">=</span><span·class="kc">True</span><span·class="p">)</span>·····<span·class="c1">#·explanation·below</span>
489	</pre></div>	489	</pre></div>
490	</div>	490	</div>
491	<p>In·the·last·example,·the·particle·was·fixed·in·space·by·the·<code·class="docutils·literal·notranslate"><span·class="pre">fixed=True</span></code>·parameter·to·<a·class="reference·external"·href="yade.utils.html#yade.utils.sphere">sphere</a>;·such·a·particle·will·not·move,·creating·a·primitive·boundary·condition.</p>	491	<p>In·the·last·example,·the·particle·was·fixed·in·space·by·the·<code·class="docutils·literal·notranslate"><span·class="pre">fixed=True</span></code>·parameter·to·<a·class="reference·external"·href="yade.utils.html#yade.utils.sphere">sphere</a>;·such·a·particle·will·not·move,·creating·a·primitive·boundary·condition.</p>
492	<p>A·particle·object·is·not·yet·part·of·the·simulation;·in·order·to·do·so,·a·special·function·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.BodyContainer.append">O.bodies.append</a>·(also·see·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.bodies">Omega::bodies</a>·and·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Scene">Scene</a>)·is·called:</p>	492	<p>A·particle·object·is·not·yet·part·of·the·simulation;·in·order·to·do·so,·a·special·function·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.BodyContainer.append">O.bodies.append</a>·(also·see·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Omega.bodies">Omega::bodies</a>·and·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Scene">Scene</a>)·is·called:</p>
493	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[49]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">bodies</span><span·class="o">.</span><span·class="n">append</span><span·class="p">(</span><span·class="n">s</span><span·class="p">)</span>············<span·class="c1">#·adds·particle·s·to·the·simulation;·returns·id·of·the·particle(s)·added</span>	493	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[49]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">bodies</span><span·class="o">.</span><span·class="n">append</span><span·class="p">(</span><span·class="n">s</span><span·class="p">)</span>············<span·class="c1">#·adds·particle·s·to·the·simulation;·returns·id·of·the·particle(s)·added</span>
494	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">49</span><span·class="p">]:</span>·<span·class="mi">23</span>	494	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">49</span><span·class="p">]:</span>·<span·class="mi">22</span>
495	</pre></div>	495	</pre></div>
496	</div>	496	</div>
497	</section>	497	</section>
498	<section·id="packs">	498	<section·id="packs">
499	<h4>Packs<a·class="headerlink"·href="#packs"·title="Link·to·this·heading">¶</a></h4>	499	<h4>Packs<a·class="headerlink"·href="#packs"·title="Link·to·this·heading">¶</a></h4>
500	<p>There·are·functions·to·generate·a·specific·arrangement·of·particles·in·the·<a·class="reference·external"·href="yade.pack.html#">pack</a>·module;·for·instance,·cloud·(random·loose·packing)·of·spheres·can·be·generated·with·the·<a·class="reference·external"·href="yade.pack.html#yade._packSpheres.SpherePack">pack.SpherePack</a>·class:</p>	500	<p>There·are·functions·to·generate·a·specific·arrangement·of·particles·in·the·<a·class="reference·external"·href="yade.pack.html#">pack</a>·module;·for·instance,·cloud·(random·loose·packing)·of·spheres·can·be·generated·with·the·<a·class="reference·external"·href="yade.pack.html#yade._packSpheres.SpherePack">pack.SpherePack</a>·class:</p>
501	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[50]:·</span><span·class="kn">from</span>·<span·class="nn">yade</span>·<span·class="kn">import</span>·<span·class="n">pack</span>	501	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[50]:·</span><span·class="kn">from</span>·<span·class="nn">yade</span>·<span·class="kn">import</span>·<span·class="n">pack</span>

502	<span·class="gp">Yade·[51]:·</span><span·class="n">sp</span><span·class="o">=</span><span·class="n">pack</span><span·class="o">.</span><span·class="n">SpherePack</span><span·class="p">()</span>···················<span·class="c1">#·create·an·empty·cloud;·SpherePack·contains·only·geometrical·information</span>	502	<span·class="gp">Yade·[51]:·</span><span·class="n">sp</span><span·class="o">=</span><span·class="n">pack</span><span·class="o">.</span><span·class="n">SpherePack</span><span·class="p">()</span>···················<span·class="c1">#·create·an·empty·cloud;·SpherePack·contains·only·geometrical·information</span>

503	<span·class="gp">Yade·[52]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">makeCloud</span><span·class="p">((</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">),(</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">),</span><span·class="n">rMean</span><span·class="o">=</span><span·class="mf">.2</span><span·class="p">)</span>·<span·class="c1">#·put·spheres·with·defined·radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)</span>	503	<span·class="gp">Yade·[52]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">makeCloud</span><span·class="p">((</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">,</span><span·class="mi">1</span><span·class="p">),(</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">,</span><span·class="mi">2</span><span·class="p">),</span><span·class="n">rMean</span><span·class="o">=</span><span·class="mf">.2</span><span·class="p">)</span>·<span·class="c1">#·put·spheres·with·defined·radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)</span>
504	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">52</span><span·class="p">]:</span>·<span·class="mi">6</span>	504	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">52</span><span·class="p">]:</span>·<span·class="mi">7</span>

505	<span·class="gp">Yade·[53]:·</span><span·class="k">for</span>·<span·class="n">c</span><span·class="p">,</span><span·class="n">r</span>·<span·class="ow">in</span>·<span·class="n">sp</span><span·class="p">:</span>·<span·class="nb">print</span><span·class="p">(</span><span·class="n">c</span><span·class="p">,</span><span·class="n">r</span><span·class="p">)</span>···············<span·class="c1">#·print·center·and·radius·of·all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)</span>	505	<span·class="gp">Yade·[53]:·</span><span·class="k">for</span>·<span·class="n">c</span><span·class="p">,</span><span·class="n">r</span>·<span·class="ow">in</span>·<span·class="n">sp</span><span·class="p">:</span>·<span·class="nb">print</span><span·class="p">(</span><span·class="n">c</span><span·class="p">,</span><span·class="n">r</span><span·class="p">)</span>···············<span·class="c1">#·print·center·and·radius·of·all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)</span>


Offset 64, 15 lines modified		Offset 64, 15 lines modified
64	Yade·[1]:·len(O.materials)	64	Yade·[1]:·len(O.materials)
65	Out[1]:·0	65	Out[1]:·0

66	Yade·[2]:·idConcrete=O.materials.append(FrictMat	66	Yade·[2]:·idConcrete=O.materials.append(FrictMat
67	(young=30e9,poisson=.2,frictionAngle=.6,label="concrete"))	67	(young=30e9,poisson=.2,frictionAngle=.6,label="concrete"))

68	Yade·[3]:·O.materials[idConcrete]	68	Yade·[3]:·O.materials[idConcrete]
69	Out[3]:·<FrictMat·instance·at·0x~~3090f3e~~0>	69	Out[3]:·<FrictMat·instance·at·0x4134dd70>

70	#·uses·the·last·defined·material	70	#·uses·the·last·defined·material
71	Yade·[4]:·O.bodies.append(sphere(center=(0,0,0),radius=1))	71	Yade·[4]:·O.bodies.append(sphere(center=(0,0,0),radius=1))
72	Out[4]:·0	72	Out[4]:·0

73	#·material·given·by·id	73	#·material·given·by·id
74	Yade·[5]:·O.bodies.append(sphere((0,0,2),1,material=idConcrete))	74	Yade·[5]:·O.bodies.append(sphere((0,0,2),1,material=idConcrete))
Offset 567, 15 lines modified		Offset 567, 15 lines modified
567	···....:·]	567	···....:·]
568	···....:	568	···....:

569	Yade·[29]:·i=createInteraction(0,1)	569	Yade·[29]:·i=createInteraction(0,1)

570	#·created·by·functors·in·InteractionLoop	570	#·created·by·functors·in·InteractionLoop
571	Yade·[30]:·i.geom,·i.phys	571	Yade·[30]:·i.geom,·i.phys
572	Out[30]:·(<ScGeom·instance·at·0x3090~~823~~0>,·<FrictPhys·instance·at·0x3~~092250~~0>)	572	Out[30]:·(<ScGeom·instance·at·0x40f04940>,·<FrictPhys·instance·at·0x3e7b0ba0>)
573	This·method·will·be·rather·slow·if·many·interactions·are·to·be·created·(the	573	This·method·will·be·rather·slow·if·many·interactions·are·to·be·created·(the
574	functor·lookup·will·be·repeated·for·each·of·them).·In·such·case,·ask·on·_\x8y_\x8a_\x8d_\x8e_\x8-	574	functor·lookup·will·be·repeated·for·each·of·them).·In·such·case,·ask·on·_\x8y_\x8a_\x8d_\x8e_\x8-
575	_\x8d_\x8e_\x8v_\x8@_\x8l_\x8i_\x8s_\x8t_\x8s_\x8._\x8l_\x8a_\x8u_\x8n_\x8c_\x8h_\x8p_\x8a_\x8d_\x8._\x8n_\x8e_\x8t·to·have·the·_\x8c_\x8r_\x8e_\x8a_\x8t_\x8e_\x8I_\x8n_\x8t_\x8e_\x8r_\x8a_\x8c_\x8t_\x8i_\x8o_\x8n·function·accept·list·of	575	_\x8d_\x8e_\x8v_\x8@_\x8l_\x8i_\x8s_\x8t_\x8s_\x8._\x8l_\x8a_\x8u_\x8n_\x8c_\x8h_\x8p_\x8a_\x8d_\x8._\x8n_\x8e_\x8t·to·have·the·_\x8c_\x8r_\x8e_\x8a_\x8t_\x8e_\x8I_\x8n_\x8t_\x8e_\x8r_\x8a_\x8c_\x8t_\x8i_\x8o_\x8n·function·accept·list·of
576	pairs·id’s·as·well.	576	pairs·id’s·as·well.
577	\x8\x8\x8·A\x8As\x8ss\x8si\x8ig\x8gn\x8ni\x8in\x8ng\x8g·c\x8co\x8oh\x8he\x8es\x8si\x8iv\x8ve\x8e·b\x8bo\x8on\x8nd\x8ds\x8s·(\x8(p\x8po\x8os\x8ss\x8si\x8ib\x8bl\x8ly\x8y·b\x8be\x8et\x8tw\x8we\x8ee\x8en\x8n·d\x8di\x8is\x8st\x8ta\x8an\x8nt\x8t·b\x8bo\x8od\x8di\x8ie\x8es\x8s)\x8)_\x8?\x8¶·\x8\x8\x8	577	\x8\x8\x8·A\x8As\x8ss\x8si\x8ig\x8gn\x8ni\x8in\x8ng\x8g·c\x8co\x8oh\x8he\x8es\x8si\x8iv\x8ve\x8e·b\x8bo\x8on\x8nd\x8ds\x8s·(\x8(p\x8po\x8os\x8ss\x8si\x8ib\x8bl\x8ly\x8y·b\x8be\x8et\x8tw\x8we\x8ee\x8en\x8n·d\x8di\x8is\x8st\x8ta\x8an\x8nt\x8t·b\x8bo\x8od\x8di\x8ie\x8es\x8s)\x8)_\x8?\x8¶·\x8\x8\x8
578	A·particular·case·of·interactions·on·demand·is·when·cohesive·strength·needs·to	578	A·particular·case·of·interactions·on·demand·is·when·cohesive·strength·needs·to
579	be·assigned·to·interactions·when·using	579	be·assigned·to·interactions·when·using
Offset 910, 19 lines modified		Offset 910, 19 lines modified
910	implementation·in·C++·is·different)·mapping·keys·to·labels.·Contrary·to·regular	910	implementation·in·C++·is·different)·mapping·keys·to·labels.·Contrary·to·regular
911	python·dictionaries·that·you·could·create,	911	python·dictionaries·that·you·could·create,
912	····*·O.tags·is·s\x8sa\x8av\x8ve\x8ed\x8d·a\x8an\x8nd\x8d·l\x8lo\x8oa\x8ad\x8de\x8ed\x8d·w\x8wi\x8it\x8th\x8h·s\x8si\x8im\x8mu\x8ul\x8la\x8at\x8ti\x8io\x8on\x8n;	912	····*·O.tags·is·s\x8sa\x8av\x8ve\x8ed\x8d·a\x8an\x8nd\x8d·l\x8lo\x8oa\x8ad\x8de\x8ed\x8d·w\x8wi\x8it\x8th\x8h·s\x8si\x8im\x8mu\x8ul\x8la\x8at\x8ti\x8io\x8on\x8n;
913	····*·O.tags·has·some·values·pre-initialized.	913	····*·O.tags·has·some·values·pre-initialized.
914	After·Yade·startup,·O.tags·contains·the·following:	914	After·Yade·startup,·O.tags·contains·the·following:
915	Yade·[45]:·dict(O.tags)·#·convert·to·real·dictionary	915	Yade·[45]:·dict(O.tags)·#·convert·to·real·dictionary
916	Out[45]:	916	Out[45]:
917	{'author':·'~(pbuilder1@codethink04-arm64)',
918	·'isoTime':·'20250727T113448',
919	·'id':·'20250727T113448p3257836',
920	·'d.id':·'20250727T113448p3257836',
921	·'~~id.d~~':·'2~~0250727T113448p3257836~~'}	917	{'author':·'second~user~(pbuilder2@i-capture-the-hostname)',
		918	·'isoTime':·'20260831T035005',
		919	·'id':·'20260831T035005p363122',
		920	·'d.id':·'20260831T035005p363122',
		921	·'id.d':·'20260831T035005p363122'}
922	··author	922	··author
923	······Real·name,·username·and·machine·as·obtained·from·your·system·at	923	······Real·name,·username·and·machine·as·obtained·from·your·system·at
924	······simulation·creation	924	······simulation·creation
925	··id	925	··id
926	······Unique·identifier·of·this·Yade·instance·(or·of·the·instance·which·created	926	······Unique·identifier·of·this·Yade·instance·(or·of·the·instance·which·created
927	······a·loaded·simulation).·It·is·composed·of·date,·time·and·process·number.	927	······a·loaded·simulation).·It·is·composed·of·date,·time·and·process·number.
928	······Useful·if·you·run·simulations·in·parallel·and·want·to·avoid·overwriting	928	······Useful·if·you·run·simulations·in·parallel·and·want·to·avoid·overwriting
Offset 1578, 20 lines modified		Offset 1578, 20 lines modified
1578	background	1578	background
1579	colorStyle.setStyle("figureGrey",True)··#·grey·levels·for·everything	1579	colorStyle.setStyle("figureGrey",True)··#·grey·levels·for·everything
1580	These·two·styles·also·have·higher·resolution·for·displaying·the·spheres.·The	1580	These·two·styles·also·have·higher·resolution·for·displaying·the·spheres.·The
1581	style·that·was·used·pre-2024·isold.·The·available·styles·are·listed	1581	style·that·was·used·pre-2024·isold.·The·available·styles·are·listed
1582	incolorStyle.styles:	1582	incolorStyle.styles:
1583	Yade·[70]:·colorStyle.styles	1583	Yade·[70]:·colorStyle.styles
1584	Out[70]:	1584	Out[70]:
1585	{'sand':·<yade.utils.YadeColorStyle·at·0xffff7~~a4f7~~380>,	1585	{'sand':·<yade.utils.YadeColorStyle·at·0xffff7018b380>,
1586	·'old':·<yade.utils.YadeColorStyle·at·0xffff7~~a56~~9810>,	1586	·'old':·<yade.utils.YadeColorStyle·at·0xffff701f9810>,
1587	·'figureColor':·<yade.utils.YadeColorStyle·at·0xffff7~~a56~~9950>,	1587	·'figureColor':·<yade.utils.YadeColorStyle·at·0xffff701f9950>,
1588	·'figureGrey':·<yade.utils.YadeColorStyle·at·0xffff7~~a4b7~~820>,	1588	·'figureGrey':·<yade.utils.YadeColorStyle·at·0xffff70143820>,
1589	·'blue':·<yade.utils.YadeColorStyle·at·0xffff7~~a58~~c180>,	1589	·'blue':·<yade.utils.YadeColorStyle·at·0xffff7021c180>,
1590	·'screenDisplayLowRes':·<yade.utils.YadeColorStyle·at·0xffff7~~a52~~a570>}	1590	·'screenDisplayLowRes':·<yade.utils.YadeColorStyle·at·0xffff701ba570>}
1591	3D·rendering·is·one·of·several·ways·to·produce·videos·of·simulations:	1591	3D·rendering·is·one·of·several·ways·to·produce·videos·of·simulations:
1592	···1.·Capture·screen·output·(the·3d·rendering·window)·during·the·simulation·−	1592	···1.·Capture·screen·output·(the·3d·rendering·window)·during·the·simulation·−
1593	······there·are·tools·available·for·that·(such·as·_\x8I_\x8s_\x8t_\x8a_\x8n_\x8b_\x8u_\x8l·or·_\x8R_\x8e_\x8c_\x8o_\x8r_\x8d_\x8M_\x8y_\x8D_\x8e_\x8s_\x8k_\x8t_\x8o_\x8p,	1593	······there·are·tools·available·for·that·(such·as·_\x8I_\x8s_\x8t_\x8a_\x8n_\x8b_\x8u_\x8l·or·_\x8R_\x8e_\x8c_\x8o_\x8r_\x8d_\x8M_\x8y_\x8D_\x8e_\x8s_\x8k_\x8t_\x8o_\x8p,
1594	······which·are·also·packaged·for·most·Linux·distributions).·The·output·is	1594	······which·are·also·packaged·for·most·Linux·distributions).·The·output·is
1595	······“what·you·see·is·what·you·get”,·with·all·the·advantages·and	1595	······“what·you·see·is·what·you·get”,·with·all·the·advantages·and
1596	······disadvantages.	1596	······disadvantages.
1597	···2.·Periodic·frame·snapshot·using·_\x8S_\x8n_\x8a_\x8p_\x8s_\x8h_\x8o_\x8t_\x8E_\x8n_\x8g_\x8i_\x8n_\x8e·(see·_\x8e_\x8x_\x8a_\x8m_\x8p_\x8l_\x8e_\x8s_\x8/_\x8t_\x8e_\x8s_\x8t_\x8/_\x8f_\x8o_\x8r_\x8c_\x8e_\x8-	1597	···2.·Periodic·frame·snapshot·using·_\x8S_\x8n_\x8a_\x8p_\x8s_\x8h_\x8o_\x8t_\x8E_\x8n_\x8g_\x8i_\x8n_\x8e·(see·_\x8e_\x8x_\x8a_\x8m_\x8p_\x8l_\x8e_\x8s_\x8/_\x8t_\x8e_\x8s_\x8t_\x8/_\x8f_\x8o_\x8r_\x8c_\x8e_\x8-


Offset 1257, 15 lines modified		Offset 1257, 15 lines modified
1257	<div·class="math·notranslate·nohighlight">	1257	<div·class="math·notranslate·nohighlight">
1258	\[\sum\frac{1}{2}\left(m_i\vec{v}_i^2+\vec{\omega}(\mat{I}\vec{\omega}^T)\right).\]</div>	1258	\[\sum\frac{1}{2}\left(m_i\vec{v}_i^2+\vec{\omega}(\mat{I}\vec{\omega}^T)\right).\]</div>
1259	<p>For·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Body.aspherical">aspherical</a>·bodies,·necessary·frame·transformations·are·applied·to·the·inertia·tensor·<span·class="math·notranslate·nohighlight">\(\mat{I}\)</span>·as·stored·in·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.State.inertia">state.inertia</a>.</p>	1259	<p>For·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.Body.aspherical">aspherical</a>·bodies,·necessary·frame·transformations·are·applied·to·the·inertia·tensor·<span·class="math·notranslate·nohighlight">\(\mat{I}\)</span>·as·stored·in·<a·class="reference·external"·href="yade.wrapper.html#yade.wrapper.State.inertia">state.inertia</a>.</p>
1260	</dd></dl>	1260	</dd></dl>

1261	<dl·class="py·function">	1261	<dl·class="py·function">
1262	<dt·class="sig·sig-object·py"·id="yade._utils.lsSimpleShape">	1262	<dt·class="sig·sig-object·py"·id="yade._utils.lsSimpleShape">
1263	<span·class="sig-prename·descclassname"><span·class="pre">yade._utils.</span></span><span·class="sig-name·descname"><span·class="pre">lsSimpleShape</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(int)shape</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">(AlignedBox3)aabb</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(float)step=0.1</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(float)smearCoeff=1.5</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(Vector2)epsilons=Vector2(0</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">0)</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(Clump)clump=<Clump</span>·<span·class="pre">instance</span>·<span·class="pre">at</span>·<span·class="pre">0x~~2e91839~~0></span></span></em><span·class="optional">]</span><span·class="optional">]</span><span·class="optional">]</span><span·class="optional">]</span><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><a·class="reference·internal"·href="yade.plot.html#yade.plot.LevelSet"·title="yade.plot.LevelSet"><span·class="pre">LevelSet</span></a></span></span><a·class="headerlink"·href="#yade._utils.lsSimpleShape"·title="Link·to·this·definition">¶</a></dt>	1263	<span·class="sig-prename·descclassname"><span·class="pre">yade._utils.</span></span><span·class="sig-name·descname"><span·class="pre">lsSimpleShape</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(int)shape</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">(AlignedBox3)aabb</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(float)step=0.1</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(float)smearCoeff=1.5</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(Vector2)epsilons=Vector2(0</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">0)</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(Clump)clump=<Clump</span>·<span·class="pre">instance</span>·<span·class="pre">at</span>·<span·class="pre">0x3f362eb0></span></span></em><span·class="optional">]</span><span·class="optional">]</span><span·class="optional">]</span><span·class="optional">]</span><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><a·class="reference·internal"·href="yade.plot.html#yade.plot.LevelSet"·title="yade.plot.LevelSet"><span·class="pre">LevelSet</span></a></span></span><a·class="headerlink"·href="#yade._utils.lsSimpleShape"·title="Link·to·this·definition">¶</a></dt>
1264	<dd><p>Creates·a·LevelSet·shape·among·pre-defined·ones.·Not·intended·to·be·used·directly,·see·levelSetBody()·instead.</p>	1264	<dd><p>Creates·a·LevelSet·shape·among·pre-defined·ones.·Not·intended·to·be·used·directly,·see·levelSetBody()·instead.</p>
1265	<dl·class="field-list·simple">	1265	<dl·class="field-list·simple">
1266	<dt·class="field-odd">Parameters<span·class="colon">:</span></dt>	1266	<dt·class="field-odd">Parameters<span·class="colon">:</span></dt>
1267	<dd·class="field-odd"><ul·class="simple">	1267	<dd·class="field-odd"><ul·class="simple">
1268	<li><p><strong>shape</strong>·(<em>int</em>)·–·a·shape·index·among·supported·choices</p></li>	1268	<li><p><strong>shape</strong>·(<em>int</em>)·–·a·shape·index·among·supported·choices</p></li>
1269	<li><p><strong>aabb</strong>·(<a·class="reference·internal"·href="yade.minieigenHP.html#yade._minieigenHP.AlignedBox3"·title="yade._minieigenHP.AlignedBox3"><em>AlignedBox3</em></a>)·–·the·axis-aligned·surrounding·box·of·the·body</p></li>	1269	<li><p><strong>aabb</strong>·(<a·class="reference·internal"·href="yade.minieigenHP.html#yade._minieigenHP.AlignedBox3"·title="yade._minieigenHP.AlignedBox3"><em>AlignedBox3</em></a>)·–·the·axis-aligned·surrounding·box·of·the·body</p></li>
1270	<li><p><strong>step</strong>·(<a·class="reference·internal"·href="yade.math.html#yade._math.HP2.Real"·title="yade._math.HP2.Real"><em>Real</em></a>)·–·the·LevelSet·grid·step·size</p></li>	1270	<li><p><strong>step</strong>·(<a·class="reference·internal"·href="yade.math.html#yade._math.HP2.Real"·title="yade._math.HP2.Real"><em>Real</em></a>)·–·the·LevelSet·grid·step·size</p></li>


Offset 892, 15 lines modified		Offset 892, 15 lines modified
892	······Compute·overall·kinetic·energy·of·the·simulation·as	892	······Compute·overall·kinetic·energy·of·the·simulation·as
893	······\[\sum\frac{1}{2}\left(m_i\vec{v}_i^2+\vec{\omega}(\mat{I}\vec	893	······\[\sum\frac{1}{2}\left(m_i\vec{v}_i^2+\vec{\omega}(\mat{I}\vec
894	······{\omega}^T)\right).\]	894	······{\omega}^T)\right).\]
895	······For·_\x8a_\x8s_\x8p_\x8h_\x8e_\x8r_\x8i_\x8c_\x8a_\x8l·bodies,·necessary·frame·transformations·are·applied·to·the	895	······For·_\x8a_\x8s_\x8p_\x8h_\x8e_\x8r_\x8i_\x8c_\x8a_\x8l·bodies,·necessary·frame·transformations·are·applied·to·the
896	······inertia·tensor·\(\mat{I}\)·as·stored·in·_\x8s_\x8t_\x8a_\x8t_\x8e_\x8._\x8i_\x8n_\x8e_\x8r_\x8t_\x8i_\x8a.	896	······inertia·tensor·\(\mat{I}\)·as·stored·in·_\x8s_\x8t_\x8a_\x8t_\x8e_\x8._\x8i_\x8n_\x8e_\x8r_\x8t_\x8i_\x8a.
897	··yade._utils.lsSimpleShape((\x8(i\x8in\x8nt\x8t)\x8)s\x8sh\x8ha\x8ap\x8pe\x8e,·(\x8(A\x8Al\x8li\x8ig\x8gn\x8ne\x8ed\x8dB\x8Bo\x8ox\x8x3\x83)\x8)a\x8aa\x8ab\x8bb\x8b[,·(\x8(f\x8fl\x8lo\x8oa\x8at\x8t)\x8)s\x8st\x8te\x8ep\x8p=\x8=0\x80.\x8.1\x81[,	897	··yade._utils.lsSimpleShape((\x8(i\x8in\x8nt\x8t)\x8)s\x8sh\x8ha\x8ap\x8pe\x8e,·(\x8(A\x8Al\x8li\x8ig\x8gn\x8ne\x8ed\x8dB\x8Bo\x8ox\x8x3\x83)\x8)a\x8aa\x8ab\x8bb\x8b[,·(\x8(f\x8fl\x8lo\x8oa\x8at\x8t)\x8)s\x8st\x8te\x8ep\x8p=\x8=0\x80.\x8.1\x81[,
898	··(\x8(f\x8fl\x8lo\x8oa\x8at\x8t)\x8)s\x8sm\x8me\x8ea\x8ar\x8rC\x8Co\x8oe\x8ef\x8ff\x8f=\x8=1\x81.\x8.5\x85[,·(\x8(V\x8Ve\x8ec\x8ct\x8to\x8or\x8r2\x82)\x8)e\x8ep\x8ps\x8si\x8il\x8lo\x8on\x8ns\x8s=\x8=V\x8Ve\x8ec\x8ct\x8to\x8or\x8r2\x82(\x8(0\x80,·0\x80)\x8)[,·(\x8(C\x8Cl\x8lu\x8um\x8mp\x8p)\x8)c\x8cl\x8lu\x8um\x8mp\x8p=\x8=<\x8<C\x8Cl\x8lu\x8um\x8mp\x8p	898	··(\x8(f\x8fl\x8lo\x8oa\x8at\x8t)\x8)s\x8sm\x8me\x8ea\x8ar\x8rC\x8Co\x8oe\x8ef\x8ff\x8f=\x8=1\x81.\x8.5\x85[,·(\x8(V\x8Ve\x8ec\x8ct\x8to\x8or\x8r2\x82)\x8)e\x8ep\x8ps\x8si\x8il\x8lo\x8on\x8ns\x8s=\x8=V\x8Ve\x8ec\x8ct\x8to\x8or\x8r2\x82(\x8(0\x80,·0\x80)\x8)[,·(\x8(C\x8Cl\x8lu\x8um\x8mp\x8p)\x8)c\x8cl\x8lu\x8um\x8mp\x8p=\x8=<\x8<C\x8Cl\x8lu\x8um\x8mp\x8p
899	··i\x8in\x8ns\x8st\x8ta\x8an\x8nc\x8ce\x8e·a\x8at\x8t·0\x80x\x8x2.2e.e9.91.18.83.39.90\x80>\x8>]]]])·→·_\x8L_\x8e_\x8v_\x8e_\x8l_\x8S_\x8e_\x8t_\x8¶	899	··i\x8in\x8ns\x8st\x8ta\x8an\x8nc\x8ce\x8e·a\x8at\x8t·0\x80x\x8x3.3f.f3.36.62.2e.eb.b0\x80>\x8>]]]])·→·_\x8L_\x8e_\x8v_\x8e_\x8l_\x8S_\x8e_\x8t_\x8¶
900	······Creates·a·LevelSet·shape·among·pre-defined·ones.·Not·intended·to·be·used	900	······Creates·a·LevelSet·shape·among·pre-defined·ones.·Not·intended·to·be·used
901	······directly,·see·levelSetBody()·instead.	901	······directly,·see·levelSetBody()·instead.
902	········Parameters:	902	········Parameters:
903	················*·s\x8sh\x8ha\x8ap\x8pe\x8e·(i\x8in\x8nt\x8t)·–·a·shape·index·among·supported·choices	903	················*·s\x8sh\x8ha\x8ap\x8pe\x8e·(i\x8in\x8nt\x8t)·–·a·shape·index·among·supported·choices
904	················*·a\x8aa\x8ab\x8bb\x8b·(_\x8A\x8A_\x8l\x8l_\x8i\x8i_\x8g\x8g_\x8n\x8n_\x8e\x8e_\x8d\x8d_\x8B\x8B_\x8o\x8o_\x8x\x8x_\x83\x83)·–·the·axis-aligned·surrounding·box·of·the	904	················*·a\x8aa\x8ab\x8bb\x8b·(_\x8A\x8A_\x8l\x8l_\x8i\x8i_\x8g\x8g_\x8n\x8n_\x8e\x8e_\x8d\x8d_\x8B\x8B_\x8o\x8o_\x8x\x8x_\x83\x83)·–·the·axis-aligned·surrounding·box·of·the
905	··················body	905	··················body
906	················*·s\x8st\x8te\x8ep\x8p·(_\x8R\x8R_\x8e\x8e_\x8a\x8a_\x8l\x8l)·–·the·LevelSet·grid·step·size	906	················*·s\x8st\x8te\x8ep\x8p·(_\x8R\x8R_\x8e\x8e_\x8a\x8a_\x8l\x8l)·–·the·LevelSet·grid·step·size


Offset 99, 75 lines modified		Offset 99, 75 lines modified
99	············Update·object·attributes·from·given·dictionary	99	············Update·object·attributes·from·given·dictionary
100	\x8\x8\x8\x8·S\x8Sh\x8ha\x8ap\x8pe\x8e_\x8?\x8¶·\x8\x8\x8\x8	100	\x8\x8\x8\x8·S\x8Sh\x8ha\x8ap\x8pe\x8e_\x8?\x8¶·\x8\x8\x8\x8
101	[digraph·Shape·{	101	[digraph·Shape·{
102	········rankdir=RL;	102	········rankdir=RL;
103	········margin="0.2,0.05";	103	········margin="0.2,0.05";
104	········"Shape"·[shape="box",fontsize=8,style="setlinewidth	104	········"Shape"·[shape="box",fontsize=8,style="setlinewidth
105	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Shape"];	105	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Shape"];
106	········"~~Clump~~"·[shape="box",fontsize=8,style="setlinewidth	106	········"Sphere"·[shape="box",fontsize=8,style="setlinewidth
107	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.~~Clump~~"];	107	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
108	········"~~Clump~~"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	108	········"Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
109	········"LevelSet"·[shape="box",fontsize=8,style="setlinewidth
110	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];
111	········"LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
112	········"Node"·[shape="box",fontsize=8,style="setlinewidth	109	········"Node"·[shape="box",fontsize=8,style="setlinewidth
113	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];	110	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];
114	········"Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	111	········"Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
115	········"DeformableElement"·[shape="box",fontsize=8,style="setlinewidth	112	········"DeformableElement"·[shape="box",fontsize=8,style="setlinewidth
116	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];	113	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];
117	········"DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth	114	········"DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
118	(0.5)"];	115	(0.5)"];
		116	········"PFacet"·[shape="box",fontsize=8,style="setlinewidth
		117	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
		118	········"PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		119	········"Wall"·[shape="box",fontsize=8,style="setlinewidth
		120	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];
		121	········"Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		122	········"Facet"·[shape="box",fontsize=8,style="setlinewidth
		123	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
		124	········"Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
119	········"GridNode"·[shape="box",fontsize=8,style="setlinewidth	125	········"GridNode"·[shape="box",fontsize=8,style="setlinewidth
120	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];	126	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];
121	········"GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	127	········"GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
122	········"Cylinder"·[shape="box",fontsize=8,style="setlinewidth
123	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
124	········"Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
125	········"DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth
126	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];
127	········"DeformableCohesiveElement"·->·"DeformableElement"
128	[arrowsize=0.5,style="setlinewidth(0.5)"];
129	········"PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth
130	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
131	········"PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
132	(0.5)"];
133	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"
134	[shape="box",fontsize=8,style="setlinewidth
135	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
136	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·-
137	>·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
138	········"ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth	128	········"ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth
139	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];	129	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];
140	········"ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth	130	········"ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth
141	(0.5)"];	131	(0.5)"];
142	········"PFacet"·[shape="box",fontsize=8,style="setlinewidth
143	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
144	········"PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
145	········"Sphere"·[shape="box",fontsize=8,style="setlinewidth
146	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
147	········"Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
148	········"Tetra"·[shape="box",fontsize=8,style="setlinewidth	132	········"Tetra"·[shape="box",fontsize=8,style="setlinewidth
149	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];	133	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];
150	········"Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	134	········"Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
151	········"Box"·[shape="box",fontsize=8,style="setlinewidth
152	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];
153	········"Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
154	········"Facet"·[shape="box",fontsize=8,style="setlinewidth
155	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
156	········"Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
157	········"Wall"·[shape="box",fontsize=8,style="setlinewidth
158	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];
159	········"Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
160	········"GridConnection"·[shape="box",fontsize=8,style="setlinewidth	135	········"GridConnection"·[shape="box",fontsize=8,style="setlinewidth
161	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridConnection"];	136	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridConnection"];
162	········"GridConnection"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	137	········"GridConnection"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		138	········"Box"·[shape="box",fontsize=8,style="setlinewidth
		139	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];
		140	········"Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		141	········"Cylinder"·[shape="box",fontsize=8,style="setlinewidth
		142	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
		143	········"Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		144	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"
		145	[shape="box",fontsize=8,style="setlinewidth
		146	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
		147	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·-
		148	>·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
163	········"Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth	149	········"Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth
164	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];	150	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];
165	········"Lin4NodeTetra"·->·"DeformableElement"	151	········"Lin4NodeTetra"·->·"DeformableElement"
166	[arrowsize=0.5,style="setlinewidth(0.5)"];	152	[arrowsize=0.5,style="setlinewidth(0.5)"];
		153	········"LevelSet"·[shape="box",fontsize=8,style="setlinewidth
		154	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];
		155	········"LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		156	········"DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth
		157	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];
		158	········"DeformableCohesiveElement"·->·"DeformableElement"
		159	[arrowsize=0.5,style="setlinewidth(0.5)"];
		160	········"Clump"·[shape="box",fontsize=8,style="setlinewidth
		161	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Clump"];
		162	········"Clump"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		163	········"PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth
		164	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
		165	········"PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
		166	(0.5)"];
167	}]	167	}]
168	Inheritance·graph·of·Shape._\x8¶	168	Inheritance·graph·of·Shape._\x8¶
169	··c\x8cl\x8la\x8as\x8ss\x8s·yade.wrapper.Shape(i\x8in\x8nh\x8he\x8er\x8ri\x8it\x8ts\x8s·S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)_\x8¶	169	··c\x8cl\x8la\x8as\x8ss\x8s·yade.wrapper.Shape(i\x8in\x8nh\x8he\x8er\x8ri\x8it\x8ts\x8s·S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)_\x8¶
170	······Geometry·of·a·body	170	······Geometry·of·a·body
171	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶	171	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶
172	············Color·for·rendering·(normalized·RGB).	172	············Color·for·rendering·(normalized·RGB).
173	········dict((\x8(S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)\x8)a\x8ar\x8rg\x8g1\x81)·→·dict·:_\x8¶	173	········dict((\x8(S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)\x8)a\x8ar\x8rg\x8g1\x81)·→·dict·:_\x8¶
Offset 897, 27 lines modified		Offset 897, 27 lines modified
897	········rankdir=RL;	897	········rankdir=RL;
898	········margin="0.2,0.05";	898	········margin="0.2,0.05";
899	········"State"·[shape="box",fontsize=8,style="setlinewidth	899	········"State"·[shape="box",fontsize=8,style="setlinewidth
900	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.State"];	900	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.State"];
901	········"ChainedState"·[shape="box",fontsize=8,style="setlinewidth	901	········"ChainedState"·[shape="box",fontsize=8,style="setlinewidth
902	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedState"];	902	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedState"];
903	········"ChainedState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	903	········"ChainedState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		904	········"CpmState"·[shape="box",fontsize=8,style="setlinewidth
		905	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CpmState"];
		906	········"CpmState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
904	········"WireState"·[shape="box",fontsize=8,style="setlinewidth	907	········"WireState"·[shape="box",fontsize=8,style="setlinewidth
905	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireState"];	908	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireState"];
906	········"WireState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	909	········"WireState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		910	········"ThermalState"·[shape="box",fontsize=8,style="setlinewidth
		911	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ThermalState"];
		912	········"ThermalState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
907	········"JCFpmState"·[shape="box",fontsize=8,style="setlinewidth	913	········"JCFpmState"·[shape="box",fontsize=8,style="setlinewidth
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1	<map·id="State"·name="State">	1	<map·id="State"·name="State">
2	<area·shape="rect"·id="node1"·href="yade.wrapper.html#yade.wrapper.State"·title="State"·alt=""·coords="25,81,97,103"/>	2	<area·shape="rect"·id="node1"·href="yade.wrapper.html#yade.wrapper.State"·title="State"·alt=""·coords="25,81,97,103"/>
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Offset 1, 21 lines modified		Offset 1, 21 lines modified
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Offset 1, 16 lines modified		Offset 1, 16 lines modified
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Offset 1, 13 lines modified		Offset 1, 13 lines modified
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Offset 1, 17 lines modified		Offset 1, 17 lines modified
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