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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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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:·42612	6	Installed-Size:·42611
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


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1	Yade·Documentation·(3rd·ed.)	1	Yade·Documentation·(3rd·ed.)

2	3rd·Edition·based·on·Yade·version·2025.2.0,·August·30,·2026	2	3rd·Edition·based·on·Yade·version·2025.2.0,·July·29,·2025

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.
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115	2.3.16·Other·classes·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·464	115	2.3.16·Other·classes·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·464
116	Yade·modules·reference·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·475	116	Yade·modules·reference·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·475
117	2.4.1·yade.bf·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·475	117	2.4.1·yade.bf·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·475
118	2.4.2·yade.bodiesHandling·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·477	118	2.4.2·yade.bodiesHandling·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·477
119	2.4.3·yade.export·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·478	119	2.4.3·yade.export·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·478
120	2.4.4·yade.geom·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·483	120	2.4.4·yade.geom·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·483
121	2.4.5·yade.gridpfacet·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·487	121	2.4.5·yade.gridpfacet·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·487
122	2.4.6·yade.libVersions·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·491	122	2.4.6·yade.libVersions·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·492
123	2.4.7·yade.linterpolation·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·495	123	2.4.7·yade.linterpolation·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·495
124	2.4.8·yade.log·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·496	124	2.4.8·yade.log·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·496
125	2.4.9·yade.math·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·497	125	2.4.9·yade.math·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·498
126	2.4.10·yade.minieigenHP·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·538	126	2.4.10·yade.minieigenHP·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·538
127	2.4.11·yade.mpy·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·620	127	2.4.11·yade.mpy·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·620
128	2.4.12·yade.pack·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·625	128	2.4.12·yade.pack·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·625
129	2.4.13·yade.plot·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·639	129	2.4.13·yade.plot·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·639
130	2.4.14·yade.polyhedra_utils·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1065	130	2.4.14·yade.polyhedra_utils·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1065
131	2.4.15·yade.post2d·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1065	131	2.4.15·yade.post2d·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1065
132	2.4.16·yade.potential_utils·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1068	132	2.4.16·yade.potential_utils·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1068
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155	3.1.5·Conventions·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1120	155	3.1.5·Conventions·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1120
156	3.1.6·Support·framework·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1125	156	3.1.6·Support·framework·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1125
157	3.1.7·Simulation·framework·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1152	157	3.1.7·Simulation·framework·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1152
158	3.1.8·Runtime·structure·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1158	158	3.1.8·Runtime·structure·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1158
159	3.1.9·Python·framework·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1159	159	3.1.9·Python·framework·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1159
160	3.1.10·Adding·a·new·python/C++·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1161	160	3.1.10·Adding·a·new·python/C++·module·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1161
161	3.1.11·Maintaining·compatibility·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1163	161	3.1.11·Maintaining·compatibility·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1163
162	3.2·Yade·on·GitLab·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1163	162	3.2·Yade·on·GitLab·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1164
163	3.2.1·Fast·checkout·(read-only)·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1163	163	3.2.1·Fast·checkout·(read-only)·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1164
164	3.2.2·Branches·on·GitLab·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1163	164	3.2.2·Branches·on·GitLab·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1164
165	3.2.3·Merge·requests·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1167	165	3.2.3·Merge·requests·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1167
166	3.2.4·Guidelines·for·pushing·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1168	166	3.2.4·Guidelines·for·pushing·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1168
167	4·Theoretical·background·and·extensions	167	4·Theoretical·background·and·extensions
168	1169	168	1169
169	4.1·DEM·formulation·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1169	169	4.1·DEM·formulation·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1169
170	4.2·CFD-DEM·coupled·simulations·with·Yade·and·OpenFOAM·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1169	170	4.2·CFD-DEM·coupled·simulations·with·Yade·and·OpenFOAM·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1169
171	4.2.1·Supported·versions·and·examples·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1169	171	4.2.1·Supported·versions·and·examples·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1169
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263	6.1·THM·short-course·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1231	263	6.1·THM·short-course·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1231
264	6.1.1·Installing·Yade·(for·Windows·and·Mac·users)·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1231	264	6.1.1·Installing·Yade·(for·Windows·and·Mac·users)·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1231
265	6.1.2·Introduction·to·Bash·and·Python·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1232	265	6.1.2·Introduction·to·Bash·and·Python·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1232
266	6.1.3·Day·1·-·Yade·Hands-on·part·1·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1238	266	6.1.3·Day·1·-·Yade·Hands-on·part·1·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1238
267	6.1.4·Day·1·-·Yade·Hands-on·part·2·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1239	267	6.1.4·Day·1·-·Yade·Hands-on·part·2·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1239
268	6.1.5·Day·2·-·Fluids·Hands-on·part·1·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1241	268	6.1.5·Day·2·-·Fluids·Hands-on·part·1·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1241
269	6.1.6·Day·3·-·Thermal·Hands-on·part·1·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1245	269	6.1.6·Day·3·-·Thermal·Hands-on·part·1·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1245
270	6.1.7·Day·3·-·Thermal·Hands-on·part·2·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1248	270	6.1.7·Day·3·-·Thermal·Hands-on·part·2·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1249
271	7·Literature	271	7·Literature
272	1253	272	1253
273	7.1·Yade·Technical·Archive·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253	273	7.1·Yade·Technical·Archive·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253
274	7.1.1·About·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253	274	7.1.1·About·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253
275	7.1.2·Contribute·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253	275	7.1.2·Contribute·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253
276	7.1.3·Contact·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253	276	7.1.3·Contact·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253
277	7.1.4·Archive·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253	277	7.1.4·Archive·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·.·1253
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]:·2~~069~~	523	Out[14]:·2134
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]:·102~~069~~	531	Out[16]:·102134
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·0x7f~~563b505~~1c0>	612	Out[28]:·<yade.wrapper.BodyContainer·at·0x7fd47ee791c0>
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·0x33128400>,	671	(<Sphere·instance·at·0x81121a0>,
672	<State·instance·at·0x~~32f~~7f9c0>,	672	<State·instance·at·0x8187e70>,
673	<FrictMat·instance·at·0x~~33071~~360>,	673	<FrictMat·instance·at·0x8184530>,
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
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Offset 34, 54 lines modified		Offset 34, 54 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	» » "PFacet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
41	» » "PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
42	» » "Node"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];	40	» » "Cylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
43	» » "Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	41	» » "Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		42	» » "PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
		43	» » "PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
44	» » "GridNode"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];	44	» » "GridNode"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];
45	» » "GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	45	» » "GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
46	» » "LevelSet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];	46	» » "DeformableElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];
47	» » "LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	47	» » "DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		48	» » "GridConnection"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridConnection"];
		49	» » "GridConnection"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
48	» » "DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];	50	» » "DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];
49	» » "DeformableCohesiveElement"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];	51	» » "DeformableCohesiveElement"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
50	» » "Sphere"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
51	» » "Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
52	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
53	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·->·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
54	» » "Tetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];
55	» » "Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
56	» » "Cylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
57	» » "Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
58	» » "Wall"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];	52	» » "Wall"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];
59	» » "Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	53	» » "Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
60	» » "ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];
61	» » "ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth(0.5)"];
62	» » "Clump"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Clump"];
63	» » "Clump"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
64	» » "Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];
65	» » "Lin4NodeTetra"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
66	» » "Facet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];	54	» » "Facet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
67	» » "Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	55	» » "Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
68	» » "DeformableElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];
69	» » "DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
70	» » "~~Subdomain~~"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.~~Subdomain~~"];	56	» » "PFacet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
71	» » "~~Subdomain~~"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	57	» » "PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
72	» » "Poten~~tialPar~~ticle"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Poten~~tialPar~~ticle"];	58	» » "Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];
73	» » "Poten~~tialPar~~ticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	59	» » "Lin4NodeTetra"·->·"DeformableElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
74	» » "FluidDomainBbox"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FluidDomainBbox"];	60	» » "FluidDomainBbox"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FluidDomainBbox"];
75	» » "FluidDomainBbox"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	61	» » "FluidDomainBbox"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		62	» » "ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];
		63	» » "ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		64	» » "Sphere"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
		65	» » "Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		66	» » "Clump"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Clump"];
		67	» » "Clump"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
76	» » "Box"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];	68	» » "Box"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];
77	» » "Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	69	» » "Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		70	» » "Subdomain"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Subdomain"];
		71	» » "Subdomain"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
78	» » "~~Grid~~Conne~~ction~~"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.~~Grid~~Conne~~ction~~"];	72	» » "Node"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];
79	» » "~~Grid~~Conne~~ction~~"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	73	» » "Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		74	» » "LevelSet"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];
		75	» » "LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		76	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
		77	» » "Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·->·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		78	» » "Tetra"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];
		79	» » "Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
80	» }	80	» }

81	..·autoclass::·Shape	81	..·autoclass::·Shape
82	» :members:	82	» :members:
83	» :undoc-members:	83	» :undoc-members:
84	» :inherited-members:	84	» :inherited-members:

Offset 195, 24 lines modified		Offset 195, 24 lines modified
195	..·graphviz::	195	..·graphviz::
196	» :caption:·Inheritance·graph·of·State.	196	» :caption:·Inheritance·graph·of·State.

197	» digraph·State·{	197	» digraph·State·{
198	» » rankdir=RL;	198	» » rankdir=RL;
199	» » margin="0.2,0.05";	199	» » margin="0.2,0.05";
200	» » "State"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.State"];	200	» » "State"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.State"];
201	» » "ThermalState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ThermalState"];
202	» » "ThermalState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
203	» » "ChainedState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedState"];	201	» » "ChainedState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedState"];
204	» » "ChainedState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	202	» » "ChainedState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
205	» » "JCFpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.JCFpmState"];
206	» » "JCFpmState"·->·"ThermalState"·[arrowsize=0.5,style="setlinewidth(0.5)"];
207	» » "WireState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireState"];
208	» » "WireState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
209	» » "CpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CpmState"];	203	» » "CpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CpmState"];
210	» » "CpmState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];	204	» » "CpmState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		205	» » "WireState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.WireState"];
		206	» » "WireState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		207	» » "ThermalState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ThermalState"];
		208	» » "ThermalState"·->·"State"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		209	» » "JCFpmState"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.JCFpmState"];
		210	» » "JCFpmState"·->·"ThermalState"·[arrowsize=0.5,style="setlinewidth(0.5)"];
211	» }	211	» }

212	..·autoclass::·State	212	..·autoclass::·State
213	» :members:	213	» :members:
214	» :undoc-members:	214	» :undoc-members:
215	» :inherited-members:	215	» :inherited-members:

Offset 251, 52 lines modified		Offset 251, 52 lines modified
251	..·graphviz::	251	..·graphviz::
252	» :caption:·Inheritance·graph·of·Material.	252	» :caption:·Inheritance·graph·of·Material.

253	» digraph·Material·{	253	» digraph·Material·{
254	» » rankdir=RL;	254	» » rankdir=RL;
255	» » margin="0.2,0.05";	255	» » margin="0.2,0.05";
256	» » "Material"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Material"];	256	» » "Material"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Material"];
		257	» » "BubbleMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.BubbleMat"];
		258	» » "BubbleMat"·->·"Material"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		259	» » "JCFpmMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.JCFpmMat"];
		260	» » "JCFpmMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
257	» » "Cohesiv~~eDeformabl~~eEl~~ement~~Material"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cohesiv~~eDeformabl~~eEl~~ement~~Material"];	261	» » "LinCohesiveElasticMaterial"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LinCohesiveElasticMaterial"];
		262	» » "LinCohesiveElasticMaterial"·->·"CohesiveDeformableElementMaterial"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		263	» » "ElastMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ElastMat"];
258	» » "~~CohesiveDeformable~~ElementMat~~erial~~"·->·"Material"·[arrowsize=0.5,style="setlinewidth(0.5)"];	264	» » "ElastMat"·->·"Material"·[arrowsize=0.5,style="setlinewidth(0.5)"];
259	» » "FrictMatCDM"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictMatCDM"];	265	» » "FrictMatCDM"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictMatCDM"];
260	» » "FrictMatCDM"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];	266	» » "FrictMatCDM"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
261	» » "CohFrictMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.CohFrictMat"];
262	» » "CohFrictMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
263	» » "I~~nel~~a~~stCo~~h~~Fric~~tMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.I~~nel~~a~~stCo~~h~~Fric~~tMat"];	267	» » "LinIsoRayleighDampElastMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LinIsoRayleighDampElastMat"];
264	» » "I~~nel~~a~~stCo~~h~~Fric~~tMat"·->·"~~Fric~~tMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];	268	» » "LinIsoRayleighDampElastMat"·->·"LinIsoElastMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
265	» » "FrictViscoMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictViscoMat"];	269	» » "FrictViscoMat"·[shape="box",fontsize=8,style="setlinewidth(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FrictViscoMat"];
266	» » "FrictViscoMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];	270	» » "FrictViscoMat"·->·"FrictMat"·[arrowsize=0.5,style="setlinewidth(0.5)"];
Max diff block lines reached; 120830/133761 bytes (90.33%) 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]:·~~2510~~	247	Out[14]:·3088

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]:·10~~2510~~	250	Out[16]:·103088

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·0x7f~~1ff95b420~~0>	341	Out[28]:·<yade.wrapper.BodyContainer·at·0x7f04a763c350>

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·0x37d~~df91~~0>,	391	(<Sphere·instance·at·0x2dd92aa0>,
392	·<State·instance·at·0x37d~~1711~~0>,	392	·<State·instance·at·0x2ddac690>,
393	·<FrictMat·instance·at·0x~~37ce8a9~~0>,	393	·<FrictMat·instance·at·0x2dd5e2c0>,
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·0x~~37d017f~~0>	478	Out[41]:·<Interaction·instance·at·0x2dcedbc0>

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·0x~~37d017f~~0>	480	Out[42]:·<Interaction·instance·at·0x2dcedbc0>

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·0x37c~~976c~~0>	485	Out[45]:·<ScGeom·instance·at·0x2dcfa570>

486	Yade·[46]:·i.phys	486	Yade·[46]:·i.phys
487	Out[46]:·<FrictPhys·instance·at·0x~~37da9d6~~0>	487	Out[46]:·<FrictPhys·instance·at·0x2de36aa0>

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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Offset 1109, 19 lines modified		Offset 1109, 19 lines modified
1109	<wire>0</wire>	1109	<wire>0</wire>
1110	<highlight>0</highlight>	1110	<highlight>0</highlight>
1111	</px>	1111	</px>
1112	</subD>	1112	</subD>
1113	<tags·class_id="6"·tracking_level="0"·version="0">	1113	<tags·class_id="6"·tracking_level="0"·version="0">
1114	<count>5</count>	1114	<count>5</count>
1115	<item_version>0</item_version>	1115	<item_version>0</item_version>
1116	<item>author=~(pbuilder1@ionos5-amd64)</item>	1116	<item>author=second~user~(pbuilder2@i-capture-the-hostname)</item>
1117	<item>isoTime=20260~~830~~T001~~547~~</item>	1117	<item>isoTime=20250729T101836</item>
1118	<item>id=20260830T001547p3203197</item>
1119	<item>d.id=20260830T001547p3203197</item>
1120	<item>id.d=20260~~830~~T001~~547~~p320~~3197~~</item>	1118	<item>id=20250729T101836p205626</item>
		1119	<item>d.id=20250729T101836p205626</item>
		1120	<item>id.d=20250729T101836p205626</item>
1121	</tags>	1121	</tags>
1122	<engines·class_id="7"·tracking_level="0"·version="0">	1122	<engines·class_id="7"·tracking_level="0"·version="0">
1123	<count>1</count>	1123	<count>1</count>
1124	<item_version>1</item_version>	1124	<item_version>1</item_version>
1125	<item·class_id="8"·tracking_level="0"·version="1">	1125	<item·class_id="8"·tracking_level="0"·version="1">
1126	<px·class_id="10"·class_name="yade::GravityEngine"·tracking_level="1"	1126	<px·class_id="10"·class_name="yade::GravityEngine"·tracking_level="1"
1127	version="0"·object_id="_4">	1127	version="0"·object_id="_4">
Offset 1840, 15 lines modified		Offset 1840, 15 lines modified
1840	Yade·[42]:·ld=LawDispatcher([Law2_ScGeom_CpmPhys_Cpm()])	1840	Yade·[42]:·ld=LawDispatcher([Law2_ScGeom_CpmPhys_Cpm()])

1841	Yade·[43]:·ld.dispMatrix()	1841	Yade·[43]:·ld.dispMatrix()
1842	Out[43]:·{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}	1842	Out[43]:·{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}

1843	#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request	1843	#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request
1844	Yade·[44]:·ld.dispFunctor(ScGridCoGeom(),CpmPhys())	1844	Yade·[44]:·ld.dispFunctor(ScGridCoGeom(),CpmPhys())
1845	Out[44]:·<Law2_ScGeom_CpmPhys_Cpm·instance·at·0x37cd3630>	1845	Out[44]:·<Law2_ScGeom_CpmPhys_Cpm·instance·at·0x2dcff6c0>

1846	Yade·[45]:·ld.dispMatrix()	1846	Yade·[45]:·ld.dispMatrix()
1847	Out[45]:	1847	Out[45]:
1848	{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',	1848	{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',
1849	·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}	1849	·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}
1850	\x8\x8\x8·O\x8Op\x8pe\x8en\x8nG\x8GL\x8L·f\x8fu\x8un\x8nc\x8ct\x8to\x8or\x8rs\x8s_\x8?\x8¶·\x8\x8\x8	1850	\x8\x8\x8·O\x8Op\x8pe\x8en\x8nG\x8GL\x8L·f\x8fu\x8un\x8nc\x8ct\x8to\x8or\x8rs\x8s_\x8?\x8¶·\x8\x8\x8
1851	OpenGL·rendering·is·being·done·also·by·1D·functors·(dispatched·for·the·type·to	1851	OpenGL·rendering·is·being·done·also·by·1D·functors·(dispatched·for·the·type·to
Offset 1980, 39 lines modified		Offset 1980, 39 lines modified
1980	Yade·[52]:·O.run(50);·O.wait()	1980	Yade·[52]:·O.run(50);·O.wait()

1981	Yade·[53]:·yade.timing.stats()	1981	Yade·[53]:·yade.timing.stats()
1982	Name····················································Count	1982	Name····················································Count
1983	Time············Rel.·time	1983	Time············Rel.·time
1984	-------------------------------------------------------------------------------	1984	-------------------------------------------------------------------------------
1985	------------------------	1985	------------------------
1986	"firstEngine"········································50·············51.~~702~~us	1986	"firstEngine"········································50·············66.593us
1987	0.76%	1987	0.85%
1988	InsertionSortCollider································25···········~~1917~~.~~782~~us	1988	InsertionSortCollider································25···········2206.614us
1989	28.30%	1989	28.06%
1990	InteractionLoop······································50···········3~~224~~.233us	1990	InteractionLoop······································50···········3678.222us
1991	47.58%	1991	46.77%
1992	GlobalStiffnessTimeStepper····························2·············~~·48.34~~us	1992	GlobalStiffnessTimeStepper····························2·············32.759us
1993	0.71%	1993	0.42%
1994	TriaxialCompressionEngine····························50············~~502~~.~~762~~us	1994	TriaxialCompressionEngine····························50············618.849us
1995	7.42%	1995	7.87%
1996	TriaxialStateRecorder·································3············209.~~918~~us	1996	TriaxialStateRecorder·································3············295.342us
1997	3.10%	1997	3.76%
1998	NewtonIntegrator·····································50············~~821~~.~~664~~us	1998	NewtonIntegrator·····································50············966.015us
1999	12.13%	1999	12.28%
2000	··forces·sync··········································50··············8.~~909~~us	2000	··forces·sync··········································50·············12.656us
2001	1.08%	2001	1.31%
2002	··motion·integration···································50············~~790~~.~~815~~us	2002	··motion·integration···································50············923.728us
2003	96.25%	2003	95.62%
2004	··sync·max·vel·········································50··············4.839us	2004	··sync·max·vel·········································50··············7.109us
2005	0.59%	2005	0.74%
2006	··terminate············································50··············2.~~531~~us	2006	··terminate············································50··············2.999us
2007	0.31%	2007	0.31%
2008	··TOTAL···············································200············~~807~~.094us	2008	··TOTAL···············································200············946.492us
2009	98.23%	2009	97.98%
2010	TOTAL·····························································6776.~~401~~us	2010	TOTAL·····························································7864.394us
2011	100.00%	2011	100.00%
2012	Exec·count·and·time·can·be·accessed·and·manipulated·through·Engine::timingInfo	2012	Exec·count·and·time·can·be·accessed·and·manipulated·through·Engine::timingInfo
2013	from·c++·or·Engine().execCount·and·Engine().execTime·properties·in·Python.	2013	from·c++·or·Engine().execCount·and·Engine().execTime·properties·in·Python.
2014	\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	2014	\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
2015	Timing·within·engines·(and·functors)·is·based·on·_\x8T_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·class·which·is·by	2015	Timing·within·engines·(and·functors)·is·based·on·_\x8T_\x8i_\x8m_\x8i_\x8n_\x8g_\x8D_\x8e_\x8l_\x8t_\x8a_\x8s·class·which·is·by
2016	default·instantiated·in·engines·and·functors·as·Engine::timingDeltas·and	2016	default·instantiated·in·engines·and·functors·as·Engine::timingDeltas·and
2017	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).	2017	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 63344, 15 lines modified		Offset 63344, 14 lines modified
63344	········"00318":·28,	63344	········"00318":·28,
63345	········"0032":·29,	63345	········"0032":·29,
63346	········"004":·[28,·44],	63346	········"004":·[28,·44],
63347	········"0045":·28,	63347	········"0045":·28,
63348	········"005":·28,	63348	········"005":·28,
63349	········"006":·28,	63349	········"006":·28,
63350	········"0065":·29,	63350	········"0065":·29,
63351	········"006894186121910284":·35,
63352	········"007":·[28,·29],	63351	········"007":·[28,·29],
63353	········"0072":·29,	63352	········"0072":·29,
63354	········"00724":·28,	63353	········"00724":·28,
63355	········"00799":·28,	63354	········"00799":·28,
63356	········"008":·[28,·29,·45],	63355	········"008":·[28,·29,·45],
63357	········"009":·[28,·29],	63356	········"009":·[28,·29],
63358	········"0099":·29,	63357	········"0099":·29,
Offset 63366, 14 lines modified		Offset 63365, 15 lines modified
63366	········"0119":·28,	63365	········"0119":·28,
63367	········"012":·[28,·29],	63366	········"012":·[28,·29],
63368	········"01274":·28,	63367	········"01274":·28,
63369	········"013":·28,	63368	········"013":·28,
63370	········"0136":·28,	63369	········"0136":·28,
63371	········"014":·[28,·29],	63370	········"014":·[28,·29],
63372	········"015":·28,	63371	········"015":·28,
		63372	········"015u":·27,
63373	········"016":·[28,·29],	63373	········"016":·[28,·29],
63374	········"017":·[28,·33],	63374	········"017":·[28,·33],
63375	········"018":·28,	63375	········"018":·28,
63376	········"019":·28,	63376	········"019":·28,
63377	········"01a":·[27,·35,·43],	63377	········"01a":·[27,·35,·43],
63378	········"02":·[13,·22,·27,·28,·33,·44,·60,·65,·67],	63378	········"02":·[13,·22,·27,·28,·33,·44,·60,·65,·67],
63379	········"020":·28,	63379	········"020":·28,
Offset 63434, 22 lines modified		Offset 63434, 22 lines modified
63434	········"0689":·28,	63434	········"0689":·28,
63435	········"07":·[28,·29,·33,·66],	63435	········"07":·[28,·29,·33,·66],
63436	········"0714":·28,	63436	········"0714":·28,
63437	········"0731":·28,	63437	········"0731":·28,
63438	········"0733":·29,	63438	········"0733":·29,
63439	········"0740":·28,	63439	········"0740":·28,
63440	········"0785":·28,	63440	········"0785":·28,
		63441	········"079601044345743999":·35,
63441	········"08":·[27,·28,·29,·47,·59,·65],	63442	········"08":·[27,·28,·29,·47,·59,·65],
63442	········"0815":·28,	63443	········"0815":·28,
63443	········"08927029208022474":·29,	63444	········"08927029208022474":·29,
63444	········"08927029908022097":·29,	63445	········"08927029908022097":·29,
63445	········"09":·[28,·29,·65],	63446	········"09":·[28,·29,·65],
63446	········"090192":·29,	63447	········"090192":·29,
63447	········"09057":·28,	63448	········"09057":·28,
63448	········"094u":·27,
63449	········"0b000011":·[60,·67],	63449	········"0b000011":·[60,·67],
63450	········"0b011":·34,	63450	········"0b011":·34,
63451	········"0b100101":·60,	63451	········"0b100101":·60,
63452	········"0b1101":·60,	63452	········"0b1101":·60,
63453	········"0e":·46,	63453	········"0e":·46,
63454	········"0e9":·[40,·44],	63454	········"0e9":·[40,·44],
63455	········"0i":·1,	63455	········"0i":·1,
Offset 63462, 49 lines modified		Offset 63462, 49 lines modified
63462	········"0x000000000051336d":·47,	63462	········"0x000000000051336d":·47,
63463	········"0x00007f0fcd0b4b23":·47,	63463	········"0x00007f0fcd0b4b23":·47,
63464	········"0x00007f0fcd87ed57":·47,	63464	········"0x00007f0fcd87ed57":·47,
63465	········"0x00007f0fcd88c7e9":·47,	63465	········"0x00007f0fcd88c7e9":·47,
63466	········"0x00007f0fcd88cb20":·47,	63466	········"0x00007f0fcd88cb20":·47,
63467	········"0x00007f0fcd8f4f7d":·47,	63467	········"0x00007f0fcd8f4f7d":·47,
63468	········"0x1c54620":·47,	63468	········"0x1c54620":·47,
		63469	········"0x2b576960":·[60,·67],
		63470	········"0x2c12f330":·66,
63469	········"0x2d06770":·27,	63471	········"0x2d06770":·27,
63470	········"0x354ddcb0":·[60,·67],
63471	········"0x~~354d~~f380":·47,	63472	········"0x2d3bfed0":·43,
63472	········"0x361f6150":·66,
63473	········"0x37c976c0":·23,
63474	········"0x37cd3630":·27,
63475	········"0x~~37ce51b~~0":·35,	63473	········"0x2d3c7b70":·35,
63476	········"0x37ce~~8a9~~0":·23,	63474	········"0x2dcedbc0":·23,
63477	········"0x37ce9040":·43,
63478	········"0x~~37d017f~~0":·23,	63475	········"0x2dcfa570":·23,
63479	········"0x37d17110":·23,
63480	········"0x37d~~a9d~~60":·23,	63476	········"0x2dcff6c0":·27,
63481	········"0x37d~~b62d~~0":·35,	63477	········"0x2dd08350":·35,
		63478	········"0x2dd5e2c0":·23,
63482	········"0x37d~~df91~~0":·23,	63479	········"0x2dd92aa0":·23,
		63480	········"0x2ddac690":·23,
63483	········"0x37e0deb0":·35,
63484	········"0x37e10ee0":·35,
63485	········"0x37e11580":·47,
63486	········"0x37e1d950":·47,
63487	········"0x38044e60":·35,
63488	········"0x380c0af0":·43,
63489	········"0x380dd0e0":·43,	63481	········"0x2ddc0100":·43,
		63482	········"0x2ddc3020":·35,
		63483	········"0x2de2ef30":·47,
		63484	········"0x2de36aa0":·23,
63490	········"0x380ea780":·43,	63485	········"0x2dea16a0":·43,
		63486	········"0x2dede5d0":·47,
		63487	········"0x2dede640":·43,
		63488	········"0x2dedf450":·35,
		63489	········"0x2df84950":·35,
		63490	········"0x2e177920":·43,
		63491	········"0x2e18f000":·47,
		63492	········"0x7f04a763c350":·23,
		63493	········"0x7f04c836f380":·47,
		63494	········"0x7f04c838a690":·47,
		63495	········"0x7f04c83d5a90":·47,
		63496	········"0x7f04c83d5bd0":·47,
63491	········"0x380f5830":·43,	63497	········"0x7f04c83f8050":·47,
		63498	········"0x7f04c83f82b0":·47,
63492	········"0x7f0fb1268710":·47,	63499	········"0x7f0fb1268710":·47,
63493	········"0x7f0fb29f2710":·47,	63500	········"0x7f0fb29f2710":·47,
63494	········"0x7f0fb31f3710":·47,	63501	········"0x7f0fb31f3710":·47,
63495	········"0x7f0fcee53700":·47,	63502	········"0x7f0fcee53700":·47,
63496	········"0x7f1e4231e440":·25,	63503	········"0x7f1e4231e440":·25,
63497	········"0x7f1ff95b4200":·23,
63498	········"0x7f2005867380":·47,
63499	········"0x7f2005886690":·47,
63500	········"0x7f20058d1a90":·47,
63501	········"0x7f20058d1bd0":·47,
63502	········"0x7f20058f8050":·47,
63503	········"0x7f20058f82b0":·47,
63504	········"0x7f20086a1490":·25,	63504	········"0x7f20086a1490":·25,
63505	········"0x7f21a8c8d3a0":·25,	63505	········"0x7f21a8c8d3a0":·25,
63506	········"0x7f3142e43440":·25,	63506	········"0x7f3142e43440":·25,
63507	········"0x7f5b61ae9440":·25,	63507	········"0x7f5b61ae9440":·25,
63508	········"0x7f622b47f490":·25,	63508	········"0x7f622b47f490":·25,
63509	········"0x7f8dc7b73440":·25,	63509	········"0x7f8dc7b73440":·25,
63510	········"0x7f9231213490":·25,	63510	········"0x7f9231213490":·25,
Offset 63539, 17 lines modified		Offset 63539, 17 lines modified
63539	········"1016":·[28,·29],	63539	········"1016":·[28,·29],
63540	········"1017":·[28,·29],	63540	········"1017":·[28,·29],
Max diff block lines reached; 21027/24822 bytes (84.71%) of diff not shown.


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">18</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>

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>	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>

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]:·18	128	Out[2]:·19

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]	131	Out[3]:·[4,·5,·6,·7,·8,·9,·10,·11,·12,·13,·14,·15,·16,·17,·18,·19,·20,·21,·22]

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~~37e10ee~~0>	324	Out[44]:·<Sphere·instance·at·0x2ddc3020>

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, 60 lines modified		Offset 340, 63 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]:·22	347	Out[49]:·23
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]:·4	357	Out[52]:·8

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(1.505177276677005072,1.301044618655746721,1.372642005739222348)·0.2
362	Vector3(1.461534345678191071,1.222821946392576686,1.767774804324121041)·0.2
363	Vector3(1.507498499884929899,1.747965510904049946,1.61908874319053897)·0.2
364	Vector3(1.4~~65205~~155~~718729557~~,1.6797591218~~4430~~9089,1.~~208845~~03~~158~~9193~~653~~)·0.2	361	Vector3(1.411694145230848463,1.426167562097298891,1.559558035019563471)·0.2
		362	Vector3(1.252877782755795755,1.681411460305506367,1.24901156457560103)·0.2
		363	Vector3(1.663980101874742212,1.660174122057307411,1.306611668153773831)·0.2
		364	Vector3(1.625546664440511657,1.769814801416935701,1.79293265323008244)·0.2
		365	Vector3(1.662079171645773013,1.22208350011030209,1.233433134798512576)·0.2
		366	Vector3(1.771362492110802656,1.359478607577437881,1.758294792491389202)·0.2
		367	Vector3(1.207723821100633144,1.278992363978870062,1.243485468473703559)·0.2
		368	Vector3(1.215734132555510882,1.796897235979266316,1.763682014010786725)·0.2

365	Yade·[54]:·sp.toSimulation()······················#·create·particles·and·add	369	Yade·[54]:·sp.toSimulation()······················#·create·particles·and·add
366	them·to·the·simulation	370	them·to·the·simulation
367	Out[54]:·[23,·24,·25,·26]	371	Out[54]:·[24,·25,·26,·27,·28,·29,·30,·31]
368	\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8	372	\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8
369	_\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	373	_\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
370	axes-aligned·cuboids·_\x8B_\x8o_\x8x)·geometries·are·typically·used·to·define·boundaries.	374	axes-aligned·cuboids·_\x8B_\x8o_\x8x)·geometries·are·typically·used·to·define·boundaries.
371	For·instance,·a·“floor”·for·the·simulation·can·be·created·like·this:	375	For·instance,·a·“floor”·for·the·simulation·can·be·created·like·this:
372	Yade·[55]:·O.bodies.append(wall(-1,axis=2))	376	Yade·[55]:·O.bodies.append(wall(-1,axis=2))
373	Out[55]:·27	377	Out[55]:·32
374	There·are·other·convenience·functions·(like·_\x8a_\x8a_\x8b_\x8b_\x8W_\x8a_\x8l_\x8l·for·creating·closed·or	378	There·are·other·convenience·functions·(like·_\x8a_\x8a_\x8b_\x8b_\x8W_\x8a_\x8l_\x8l·for·creating·closed·or
375	open·rectangular·box,·or·family·of·_\x8y_\x8m_\x8p_\x8o_\x8r_\x8t·functions)	379	open·rectangular·box,·or·family·of·_\x8y_\x8m_\x8p_\x8o_\x8r_\x8t·functions)
376	\x8\x8\x8\x8·L\x8Lo\x8oo\x8ok\x8k·i\x8in\x8ns\x8si\x8id\x8de\x8e_\x8?\x8¶·\x8\x8\x8\x8	380	\x8\x8\x8\x8·L\x8Lo\x8oo\x8ok\x8k·i\x8in\x8ns\x8si\x8id\x8de\x8e_\x8?\x8¶·\x8\x8\x8\x8
377	The·simulation·can·be·inspected·in·several·ways.·All·data·can·be·accessed·from	381	The·simulation·can·be·inspected·in·several·ways.·All·data·can·be·accessed·from
378	python·directly:	382	python·directly:
379	Yade·[56]:·len(O.bodies)	383	Yade·[56]:·len(O.bodies)
380	Out[56]:·28	384	Out[56]:·33

381	Yade·[57]:·O.bodies[10].shape.radius···#·radius·of·body·#10·(will·give·error·if	385	Yade·[57]:·O.bodies[10].shape.radius···#·radius·of·body·#10·(will·give·error·if
382	not·sphere,·since·only·spheres·have·radius·defined)	386	not·sphere,·since·only·spheres·have·radius·defined)
383	Out[57]:·0.16	387	Out[57]:·0.16

384	Yade·[58]:·O.bodies[12].state.pos······#·position·of·body·#12	388	Yade·[58]:·O.bodies[12].state.pos······#·position·of·body·#12
		389	Out[58]:·Vector3(1.079601044345743999,1.9092028530819114,1.554809371038829102)
385	Out[58]:·Vector3
386	(1.958315791909171377,1.006894186121910284,1.387573475427218206)
387	Besides·that,·Yade·says·this·at·startup·(the·line·preceding·the·command-line):	390	Besides·that,·Yade·says·this·at·startup·(the·line·preceding·the·command-line):
388	[[·^L·clears·screen,·^U·kills·line.·F12·controller,·F11·3d·view,·F10·both,·F9	391	[[·^L·clears·screen,·^U·kills·line.·F12·controller,·F11·3d·view,·F10·both,·F9
389	generator,·F8·plot.·]]	392	generator,·F8·plot.·]]
390	··Controller	393	··Controller
391	······Pressing·F12·brings·up·a·window·for·controlling·the·simulation.·Although	394	······Pressing·F12·brings·up·a·window·for·controlling·the·simulation.·Although
392	······typically·no·human·intervention·is·done·in·large·simulations·(which·run	395	······typically·no·human·intervention·is·done·in·large·simulations·(which·run
393	······“headless”,·without·any·graphical·interaction),·it·can·be·handy·in·small	396	······“headless”,·without·any·graphical·interaction),·it·can·be·handy·in·small
Offset 410, 16 lines modified		Offset 413, 16 lines modified
410	······C\x8Co\x8on\x8nt\x8tr\x8ro\x8ol\x8ll\x8le\x8er\x8r.·It·shows·(and·updates)·internal·data·of·the·current	413	······C\x8Co\x8on\x8nt\x8tr\x8ro\x8ol\x8ll\x8le\x8er\x8r.·It·shows·(and·updates)·internal·data·of·the·current
411	······simulation.·In·particular,·one·can·have·a·look·at·engines,·particles	414	······simulation.·In·particular,·one·can·have·a·look·at·engines,·particles
412	······(B\x8Bo\x8od\x8di\x8ie\x8es\x8s)·and·interactions·(I\x8In\x8nt\x8te\x8er\x8ra\x8ac\x8ct\x8ti\x8io\x8on\x8ns\x8s).·Clicking·at·each·of·the	415	······(B\x8Bo\x8od\x8di\x8ie\x8es\x8s)·and·interactions·(I\x8In\x8nt\x8te\x8er\x8ra\x8ac\x8ct\x8ti\x8io\x8on\x8ns\x8s).·Clicking·at·each·of·the
413	······attribute·names·links·to·the·appropriate·section·in·the·documentation.	416	······attribute·names·links·to·the·appropriate·section·in·the·documentation.
414	Exercises	417	Exercises
415	···1.·What·is·this·code·going·to·do?	418	···1.·What·is·this·code·going·to·do?
416	······Yade·[59]:·O.bodies.append([sphere((2*i,0,0),1)·for·i·in·range(1,20)])	419	······Yade·[59]:·O.bodies.append([sphere((2*i,0,0),1)·for·i·in·range(1,20)])
417	······Out[59]:·[28,·29,·30,·31,·32,·33,·34,·35,·36,·37,·38,·39,·40,·41,·42,·43,	420	······Out[59]:·[33,·34,·35,·36,·37,·38,·39,·40,·41,·42,·43,·44,·45,·46,·47,·48,
418	······44,·45,·46]	421	······49,·50,·51]
419	···2.·Create·a·simple·simulation·with·cloud·of·spheres·enclosed·in·the·box	422	···2.·Create·a·simple·simulation·with·cloud·of·spheres·enclosed·in·the·box
420	······(0,0,0)·and·(1,1,1)·with·mean·radius·.1.·(hint:	423	······(0,0,0)·and·(1,1,1)·with·mean·radius·.1.·(hint:
421	······_\x8p_\x8a_\x8c_\x8k_\x8._\x8S_\x8p_\x8h_\x8e_\x8r_\x8e_\x8P_\x8a_\x8c_\x8k_\x8._\x8m_\x8a_\x8k_\x8e_\x8C_\x8l_\x8o_\x8u_\x8d)	424	······_\x8p_\x8a_\x8c_\x8k_\x8._\x8S_\x8p_\x8h_\x8e_\x8r_\x8e_\x8P_\x8a_\x8c_\x8k_\x8._\x8m_\x8a_\x8k_\x8e_\x8C_\x8l_\x8o_\x8u_\x8d)
422	···3.·Enclose·the·cloud·created·above·in·box·with·corners·(0,0,0)·and·(1,1,1);	425	···3.·Enclose·the·cloud·created·above·in·box·with·corners·(0,0,0)·and·(1,1,1);
423	······keep·the·top·of·the·box·open.·(hint:·_\x8a_\x8a_\x8b_\x8b_\x8W_\x8a_\x8l_\x8l;·type·aabbWall?·or	426	······keep·the·top·of·the·box·open.·(hint:·_\x8a_\x8a_\x8b_\x8b_\x8W_\x8a_\x8l_\x8l;·type·aabbWall?·or
424	······aabbWall??·to·get·help·on·the·command·line)	427	······aabbWall??·to·get·help·on·the·command·line)
425	···4.·Open·the·3D·view,·try·zooming·in/out;·position·axes·so·that·\(z\)·is	428	···4.·Open·the·3D·view,·try·zooming·in/out;·position·axes·so·that·\(z\)·is
Offset 440, 18 lines modified		Offset 443, 18 lines modified
440	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#	443	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#
441	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
442	···....:·]	445	···....:·]
443	···....:	446	···....:

444	Yade·[61]:·O.engines	447	Yade·[61]:·O.engines
445	Out[61]:	448	Out[61]:
446	[<ForceResetter·instance·at·0x~~37db62d~~0>,	449	[<ForceResetter·instance·at·0x2dedf450>,
447	·<InsertionSortCollider·instance·at·0x~~3804~~4e60>,	450	·<InsertionSortCollider·instance·at·0x2df84950>,
448	·<InteractionLoop·instance·at·0x~~37ce51b~~0>,	451	·<InteractionLoop·instance·at·0x2dd08350>,
449	·<NewtonIntegrator·instance·at·0x~~37e0deb~~0>]	452	·<NewtonIntegrator·instance·at·0x2d3c7b70>]

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

452	Yade·[63]:·newtonCustomLabel.damping	455	Yade·[63]:·newtonCustomLabel.damping
453	Out[63]:·0.2	456	Out[63]:·0.2
454	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


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3	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/	3	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/
4	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/	4	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/
5	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/	5	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/
6	-rw-r--r--···0·root·········(0)·root·········(0)·11177919·2025-02-10·05:43:53.000000·./usr/share/doc/yade/Yade.pdf	6	-rw-r--r--···0·root·········(0)·root·········(0)·11178962·2025-02-10·05:43:53.000000·./usr/share/doc/yade/Yade.pdf
7	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/	7	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/
8	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-double/	8	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-double/
9	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-double/img/	9	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-double/img/
10	-rw-r--r--···0·root·········(0)·root·········(0)····35719·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-double/img/yade-logo-note.png	10	-rw-r--r--···0·root·········(0)·root·········(0)····35719·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-double/img/yade-logo-note.png
11	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-float128/	11	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-float128/
12	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-float128/img/	12	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-float128/img/
13	-rw-r--r--···0·root·········(0)·root·········(0)····35719·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-float128/img/yade-logo-note.png	13	-rw-r--r--···0·root·········(0)·root·········(0)····35719·2025-02-10·05:43:53.000000·./usr/share/doc/yade/doc/yade-float128/img/yade-logo-note.png
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42	-rw-r--r--···0·root·········(0)·root·········(0)····65595·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/connect.png	42	-rw-r--r--···0·root·········(0)·root·········(0)····65595·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/connect.png
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44	-rw-r--r--···0·root·········(0)·root·········(0)····34276·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/funnel.png	44	-rw-r--r--···0·root·········(0)·root·········(0)····34276·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/funnel.png
45	-rw-r--r--···0·root·········(0)·root·········(0)····12145·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/gnuplot.png	45	-rw-r--r--···0·root·········(0)·root·········(0)····12145·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/gnuplot.png
46	-rw-r--r--···0·root·········(0)·root·········(0)·····2604·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-026e1bdf412147766472ddfdaf48b32402babcac.png	46	-rw-r--r--···0·root·········(0)·root·········(0)·····2604·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-026e1bdf412147766472ddfdaf48b32402babcac.png
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48	-rw-r--r--···0·root·········(0)·root·········(0)····44759·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-05d4~~f6ac9~~78f~~64659~~10~~3cc1~~62~~cd8196967527519~~.png	48	-rw-r--r--···0·root·········(0)·root·········(0)····11701·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-0cea0487247278dff3b9610f277de7f7fc2e36dd.png
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50	-rw-r--r--···0·root·········(0)·root·········(0)···~~·48688~~·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-065~~f09ef6f33464~~e8~~d0c~~7~~a124~~a~~a2372c935c~~4~~5f7~~.png	50	-rw-r--r--···0·root·········(0)·root·········(0)···177895·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-0cea41bbc92a9e8f2f7ca55af599c4d7274d636a.png
51	-rw-r--r--···0·root·········(0)·root·········(0)·····~~2340~~·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-065~~f09ef6f33464~~e8~~d0c~~7~~a124~~a~~a2372c935c~~4~~5f7~~.png.map	51	-rw-r--r--···0·root·········(0)·root·········(0)·····6136·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-0cea41bbc92a9e8f2f7ca55af599c4d7274d636a.png.map
52	-rw-r--r--···0·root·········(0)·root·········(0)·····5~~350~~·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-07f68c81e~~5d00090b~~e4~~fd0~~e~~6c16c323d~~a~~192a1fc~~.png	52	-rw-r--r--···0·root·········(0)·root·········(0)·····5911·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-17f9812096113ae486215e7db30e452a557e728d.png
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54	-rw-r--r--···0·root·········(0)·root·········(0)···~~·54941~~·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-1627527bc~~711~~107ccf~~a7d~~0~~a22bf665e2~~3~~b8db2af~~.png	60	-rw-r--r--···0·root·········(0)·root·········(0)···126060·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-2cee16c7279ccd766f4ae0d03c4a28a9333ae745.png
55	-rw-r--r--···0·root·········(0)·root·········(0)·····~~2869~~·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-1627527bc~~711~~107ccf~~a7d~~0~~a22bf665e2~~3~~b8db2af~~.png.map	61	-rw-r--r--···0·root·········(0)·root·········(0)·····4780·2025-02-10·05:43:53.000000·./usr/share/doc/yade/html/_images/graphviz-2cee16c7279ccd766f4ae0d03c4a28a9333ae745.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">~~2510~~</span>	361	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">14</span><span·class="p">]:</span>·<span·class="mi">3088</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">10~~2510~~</span>	364	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">16</span><span·class="p">]:</span>·<span·class="mi">103088</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">0x7f~~1ff95b420~~0</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">0x7f04a763c350</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>


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1264	<span·class="w">»»»»</span><span·class="nt"><wire></span>0<span·class="nt"></wire></span>	1264	<span·class="w">»»»»</span><span·class="nt"><wire></span>0<span·class="nt"></wire></span>
1265	<span·class="w">»»»»</span><span·class="nt"><highlight></span>0<span·class="nt"></highlight></span>	1265	<span·class="w">»»»»</span><span·class="nt"><highlight></span>0<span·class="nt"></highlight></span>
1266	<span·class="w">»»»</span><span·class="nt"></px></span>	1266	<span·class="w">»»»</span><span·class="nt"></px></span>
1267	<span·class="w">»»</span><span·class="nt"></subD></span>	1267	<span·class="w">»»</span><span·class="nt"></subD></span>
1268	<span·class="w">»»</span><span·class="nt"><tags</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"6"</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>	1268	<span·class="w">»»</span><span·class="nt"><tags</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"6"</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>
1269	<span·class="w">»»»</span><span·class="nt"><count></span>5<span·class="nt"></count></span>	1269	<span·class="w">»»»</span><span·class="nt"><count></span>5<span·class="nt"></count></span>
1270	<span·class="w">»»»</span><span·class="nt"><item_version></span>0<span·class="nt"></item_version></span>	1270	<span·class="w">»»»</span><span·class="nt"><item_version></span>0<span·class="nt"></item_version></span>
1271	<span·class="w">»»»</span><span·class="nt"><item></span>author=~(pbuilder1@ionos5-amd64)<span·class="nt"></item></span>	1271	<span·class="w">»»»</span><span·class="nt"><item></span>author=second~user~(pbuilder2@i-capture-the-hostname)<span·class="nt"></item></span>
1272	<span·class="w">»»»</span><span·class="nt"><item></span>isoTime=20260~~830~~T001~~547~~<span·class="nt"></item></span>	1272	<span·class="w">»»»</span><span·class="nt"><item></span>isoTime=20250729T101836<span·class="nt"></item></span>
1273	<span·class="w">»»»</span><span·class="nt"><item></span>id=20260~~830~~T001~~547~~p320~~3197~~<span·class="nt"></item></span>	1273	<span·class="w">»»»</span><span·class="nt"><item></span>id=20250729T101836p205626<span·class="nt"></item></span>
1274	<span·class="w">»»»</span><span·class="nt"><item></span>d.id=20260~~830~~T001~~547~~p320~~3197~~<span·class="nt"></item></span>	1274	<span·class="w">»»»</span><span·class="nt"><item></span>d.id=20250729T101836p205626<span·class="nt"></item></span>
1275	<span·class="w">»»»</span><span·class="nt"><item></span>id.d=20260~~830~~T001~~547~~p320~~3197~~<span·class="nt"></item></span>	1275	<span·class="w">»»»</span><span·class="nt"><item></span>id.d=20250729T101836p205626<span·class="nt"></item></span>
1276	<span·class="w">»»</span><span·class="nt"></tags></span>	1276	<span·class="w">»»</span><span·class="nt"></tags></span>
1277	<span·class="w">»»</span><span·class="nt"><engines</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"7"</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>	1277	<span·class="w">»»</span><span·class="nt"><engines</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"7"</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>
1278	<span·class="w">»»»</span><span·class="nt"><count></span>1<span·class="nt"></count></span>	1278	<span·class="w">»»»</span><span·class="nt"><count></span>1<span·class="nt"></count></span>
1279	<span·class="w">»»»</span><span·class="nt"><item_version></span>1<span·class="nt"></item_version></span>	1279	<span·class="w">»»»</span><span·class="nt"><item_version></span>1<span·class="nt"></item_version></span>
1280	<span·class="w">»»»</span><span·class="nt"><item</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">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"1"</span><span·class="nt">></span>	1280	<span·class="w">»»»</span><span·class="nt"><item</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">"0"</span><span·class="w">·</span><span·class="na">version=</span><span·class="s">"1"</span><span·class="nt">></span>
1281	<span·class="w">»»»»</span><span·class="nt"><px</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"10"</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">"_4"</span><span·class="nt">></span>	1281	<span·class="w">»»»»</span><span·class="nt"><px</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"10"</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">"_4"</span><span·class="nt">></span>
1282	<span·class="w">»»»»»</span><span·class="nt"><FieldApplier</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"11"</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">"_5"</span><span·class="nt">></span>	1282	<span·class="w">»»»»»</span><span·class="nt"><FieldApplier</span><span·class="w">·</span><span·class="na">class_id=</span><span·class="s">"11"</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">"_5"</span><span·class="nt">></span>
Offset 1945, 15 lines modified		Offset 1945, 15 lines modified
1945	<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>	1945	<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>

1946	<span·class="gp">Yade·[43]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>	1946	<span·class="gp">Yade·[43]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>
1947	<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>	1947	<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>

1948	<span·class="c">#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request</span>	1948	<span·class="c">#·see·how·the·entry·for·ScGridCoGeom·will·be·filled·after·this·request</span>
1949	<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>	1949	<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>
1950	<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">0x37cd3630</span><span·class="o">></span>	1950	<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">0x2dcff6c0</span><span·class="o">></span>

1951	<span·class="gp">Yade·[45]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>	1951	<span·class="gp">Yade·[45]:·</span><span·class="n">ld</span><span·class="o">.</span><span·class="n">dispMatrix</span><span·class="p">()</span>
1952	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">45</span><span·class="p">]:</span>·	1952	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">45</span><span·class="p">]:</span>·
1953	<span·class="go">{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',</span>	1953	<span·class="go">{('GenericSpheresContact',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm',</span>
1954	<span·class="go">·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}</span>	1954	<span·class="go">·('ScGridCoGeom',·'CpmPhys'):·'Law2_ScGeom_CpmPhys_Cpm'}</span>
1955	</pre></div>	1955	</pre></div>
1956	</div>	1956	</div>
Offset 2073, 27 lines modified		Offset 2073, 27 lines modified
2073	<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>	2073	<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~~37e10ee~~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">0x2ddc3020</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, 61 lines modified		Offset 488, 65 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">22</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>
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">4</span>	504	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">52</span><span·class="p">]:</span>·<span·class="mi">8</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 269, 15 lines modified		Offset 269, 15 lines modified
269	<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>	269	<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>
270	<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>	270	<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>
271	</ol>	271	</ol>
272	<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>.</p>	272	<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>.</p>
273	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[8]:·</span><span·class="n">s</span><span·class="o">=</span><span·class="n">utils</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>	273	<div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">Yade·[8]:·</span><span·class="n">s</span><span·class="o">=</span><span·class="n">utils</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>

274	<span·class="gp">Yade·[9]:·</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>	274	<span·class="gp">Yade·[9]:·</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>
275	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">9</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">0x37ce9040</span><span·class="o">></span>	275	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">9</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">0x2ddc0100</span><span·class="o">></span>

276	<span·class="gp">Yade·[10]:·</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>	276	<span·class="gp">Yade·[10]:·</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>
277	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">10</span><span·class="p">]:</span>·<span·class="mf">1.0</span>	277	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">10</span><span·class="p">]:</span>·<span·class="mf">1.0</span>

278	<span·class="gp">Yade·[11]:·</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>	278	<span·class="gp">Yade·[11]:·</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>
279	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">11</span><span·class="p">]:</span>·	279	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">11</span><span·class="p">]:</span>·
280	<span·class="go">(4188.790204786391,</span>	280	<span·class="go">(4188.790204786391,</span>
Offset 304, 20 lines modified		Offset 304, 20 lines modified
304	<span·class="gp">Yade·[16]:·</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>	304	<span·class="gp">Yade·[16]:·</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>

305	<span·class="gp">Yade·[17]:·</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>	305	<span·class="gp">Yade·[17]:·</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>
306	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">17</span><span·class="p">]:</span>·<span·class="mi">6</span>	306	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">17</span><span·class="p">]:</span>·<span·class="mi">6</span>

307	<span·class="gp">Yade·[18]:·</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>	307	<span·class="gp">Yade·[18]:·</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>
308	<span·class="gp">···....:</span>·	308	<span·class="gp">···....:</span>·
309	<span·class="go">Vector3(1.615327221272915059,1.457126136965635865,1.365840945236695969)·0.2</span>
310	<span·class="go">Vector3(1.351919413967893835,1.571036257306665851,1.739256663944175774)·0.2</span>
311	<span·class="go">Vector3(1.394661745813322806,1.791511808412102447,1.400181626818785441)·0.2</span>
312	<span·class="go">Vector3(1.735137412964274706,1.209893937268739617,1.767581342282109835)·0.2</span>
313	<span·class="go">Vector3(1.788372887392994492,1.789274515306601199,1.594968247452060339)·0.2</span>
314	<span·class="go">Vector3(1.259727544~~0423~~15683,1.~~201~~0~~10499~~7~~196~~5~~5122~~,1.35~~4782917217611~~793)·0.2</span>	309	<span·class="go">Vector3(1.359885287815862709,1.643052513743959553,1.255864680439390479)·0.2</span>
		310	<span·class="go">Vector3(1.681459210175057395,1.79777659880626306,1.499436183693946933)·0.2</span>
		311	<span·class="go">Vector3(1.202137322132764918,1.599232833887923144,1.656233136323434385)·0.2</span>
		312	<span·class="go">Vector3(1.547908037529849068,1.24396242915871369,1.235171994402539664)·0.2</span>
		313	<span·class="go">Vector3(1.616138175611168348,1.387770286755724003,1.742043060384973696)·0.2</span>
		314	<span·class="go">Vector3(1.204348075970371745,1.202828930739873181,1.485414788882438053)·0.2</span>

315	<span·class="gp">Yade·[19]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">toSimulation</span><span·class="p">()</span>······················<span·class="c1">#·create·particles·and·add·them·to·the·simulation</span>	315	<span·class="gp">Yade·[19]:·</span><span·class="n">sp</span><span·class="o">.</span><span·class="n">toSimulation</span><span·class="p">()</span>······················<span·class="c1">#·create·particles·and·add·them·to·the·simulation</span>
316	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">19</span><span·class="p">]:</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">3</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>	316	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">19</span><span·class="p">]:</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">3</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>
317	</pre></div>	317	</pre></div>
318	</div>	318	</div>
319	</section>	319	</section>
320	<section·id="boundaries">	320	<section·id="boundaries">
Offset 378, 18 lines modified		Offset 378, 18 lines modified
378	<span·class="gp">···....:</span>····<span·class="p">),</span>	378	<span·class="gp">···....:</span>····<span·class="p">),</span>
379	<span·class="gp">···....:</span>····<span·class="n">NewtonIntegrator</span><span·class="p">(</span><span·class="n">damping</span><span·class="o">=</span><span·class="mf">.2</span><span·class="p">,</span><span·class="n">label</span><span·class="o">=</span><span·class="s1">'newtonCustomLabel'</span><span·class="p">)</span>······<span·class="c1">#·define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily</span>	379	<span·class="gp">···....:</span>····<span·class="n">NewtonIntegrator</span><span·class="p">(</span><span·class="n">damping</span><span·class="o">=</span><span·class="mf">.2</span><span·class="p">,</span><span·class="n">label</span><span·class="o">=</span><span·class="s1">'newtonCustomLabel'</span><span·class="p">)</span>······<span·class="c1">#·define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily</span>
380	<span·class="gp">···....:</span>·<span·class="p">]</span>	380	<span·class="gp">···....:</span>·<span·class="p">]</span>
381	<span·class="gp">···....:</span>·	381	<span·class="gp">···....:</span>·

382	<span·class="gp">Yade·[25]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span>	382	<span·class="gp">Yade·[25]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span>
383	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">25</span><span·class="p">]:</span>·	383	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">25</span><span·class="p">]:</span>·
384	<span·class="go">[<ForceResetter·instance·at·0x~~380f583~~0>,</span>	384	<span·class="go">[<ForceResetter·instance·at·0x2e177920>,</span>
385	<span·class="go">·<InsertionSortCollider·instance·at·0x~~380dd0e~~0>,</span>	385	<span·class="go">·<InsertionSortCollider·instance·at·0x2dea16a0>,</span>
386	<span·class="go">·<InteractionLoop·instance·at·0x~~380ea78~~0>,</span>	386	<span·class="go">·<InteractionLoop·instance·at·0x2dede640>,</span>
387	<span·class="go">·<NewtonIntegrator·instance·at·0x~~380c0af~~0>]</span>	387	<span·class="go">·<NewtonIntegrator·instance·at·0x2d3bfed0>]</span>

388	<span·class="gp">Yade·[26]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span><span·class="p">[</span><span·class="o">-</span><span·class="mi">1</span><span·class="p">]</span><span·class="o">==</span><span·class="n">newtonCustomLabel</span>····<span·class="c1">#·is·it·the·same·object?</span>	388	<span·class="gp">Yade·[26]:·</span><span·class="n">O</span><span·class="o">.</span><span·class="n">engines</span><span·class="p">[</span><span·class="o">-</span><span·class="mi">1</span><span·class="p">]</span><span·class="o">==</span><span·class="n">newtonCustomLabel</span>····<span·class="c1">#·is·it·the·same·object?</span>
389	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">26</span><span·class="p">]:</span>·<span·class="kc">True</span>	389	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">26</span><span·class="p">]:</span>·<span·class="kc">True</span>

390	<span·class="gp">Yade·[27]:·</span><span·class="n">newtonCustomLabel</span><span·class="o">.</span><span·class="n">damping</span>	390	<span·class="gp">Yade·[27]:·</span><span·class="n">newtonCustomLabel</span><span·class="o">.</span><span·class="n">damping</span>
391	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">27</span><span·class="p">]:</span>·<span·class="mf">0.2</span>	391	<span·class="gr">Out</span><span·class="p">[</span><span·class="mi">27</span><span·class="p">]:</span>·<span·class="mf">0.2</span>
392	</pre></div>	392	</pre></div>


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·0x37ce9040>	138	Out[9]:·<Sphere·instance·at·0x2ddc0100>

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 172, 20 lines modified		Offset 172, 20 lines modified
172	Yade·[17]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.2)·#·put·spheres·with·defined	172	Yade·[17]:·sp.makeCloud((1,1,1),(2,2,2),rMean=.2)·#·put·spheres·with·defined
173	radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)	173	radius·inside·box·given·by·corners·(1,1,1)·and·(2,2,2)
174	Out[17]:·6	174	Out[17]:·6

175	Yade·[18]:·for·c,r·in·sp:·print(c,r)···············#·print·center·and·radius·of	175	Yade·[18]:·for·c,r·in·sp:·print(c,r)···············#·print·center·and·radius·of
176	all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)	176	all·particles·(SpherePack·is·a·sequence·which·can·be·iterated·over)
177	···....:	177	···....:
178	Vector3(1.615327221272915059,1.457126136965635865,1.365840945236695969)·0.2
179	Vector3(1.351919413967893835,1.571036257306665851,1.739256663944175774)·0.2
180	Vector3(1.394661745813322806,1.791511808412102447,1.400181626818785441)·0.2
181	Vector3(1.735137412964274706,1.209893937268739617,1.767581342282109835)·0.2
182	Vector3(1.788372887392994492,1.789274515306601199,1.594968247452060339)·0.2
183	Vector3(1.259727544~~0423~~15683,1.~~201~~0~~10499~~7~~196~~5~~5122~~,1.35~~4782917217611~~793)·0.2	178	Vector3(1.359885287815862709,1.643052513743959553,1.255864680439390479)·0.2
		179	Vector3(1.681459210175057395,1.79777659880626306,1.499436183693946933)·0.2
		180	Vector3(1.202137322132764918,1.599232833887923144,1.656233136323434385)·0.2
		181	Vector3(1.547908037529849068,1.24396242915871369,1.235171994402539664)·0.2
		182	Vector3(1.616138175611168348,1.387770286755724003,1.742043060384973696)·0.2
		183	Vector3(1.204348075970371745,1.202828930739873181,1.485414788882438053)·0.2

184	Yade·[19]:·sp.toSimulation()······················#·create·particles·and·add	184	Yade·[19]:·sp.toSimulation()······················#·create·particles·and·add
185	them·to·the·simulation	185	them·to·the·simulation
186	Out[19]:·[1,·2,·3,·4,·5,·6]	186	Out[19]:·[1,·2,·3,·4,·5,·6]
187	\x8\x8\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8\x8\x8	187	\x8\x8\x8\x8\x8·B\x8Bo\x8ou\x8un\x8nd\x8da\x8ar\x8ri\x8ie\x8es\x8s_\x8?\x8¶·\x8\x8\x8\x8\x8
188	_\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	_\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	geometries·are·typically·used·to·define·boundaries.·For·instance,·a·“floor”·for	189	geometries·are·typically·used·to·define·boundaries.·For·instance,·a·“floor”·for
Offset 262, 18 lines modified		Offset 262, 18 lines modified
262	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#	262	···....:····NewtonIntegrator(damping=.2,label='newtonCustomLabel')······#
263	define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily	263	define·a·label·newtonCustomLabel·under·which·we·can·access·this·engine·easily
264	···....:·]	264	···....:·]
265	···....:	265	···....:

266	Yade·[25]:·O.engines	266	Yade·[25]:·O.engines
267	Out[25]:	267	Out[25]:
268	[<ForceResetter·instance·at·0x~~380f583~~0>,	268	[<ForceResetter·instance·at·0x2e177920>,
269	·<InsertionSortCollider·instance·at·0x~~380dd0e~~0>,	269	·<InsertionSortCollider·instance·at·0x2dea16a0>,
270	·<InteractionLoop·instance·at·0x~~380ea78~~0>,	270	·<InteractionLoop·instance·at·0x2dede640>,
271	·<NewtonIntegrator·instance·at·0x~~380c0af~~0>]	271	·<NewtonIntegrator·instance·at·0x2d3bfed0>]

272	Yade·[26]:·O.engines[-1]==newtonCustomLabel····#·is·it·the·same·object?	272	Yade·[26]:·O.engines[-1]==newtonCustomLabel····#·is·it·the·same·object?
273	Out[26]:·True	273	Out[26]:·True

274	Yade·[27]:·newtonCustomLabel.damping	274	Yade·[27]:·newtonCustomLabel.damping
275	Out[27]:·0.2	275	Out[27]:·0.2
276	Instead·of·typing·everything·into·the·command-line,·one·can·describe·simulation	276	Instead·of·typing·everything·into·the·command-line,·one·can·describe·simulation


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·0x37e11580>	69	Out[3]:·<FrictMat·instance·at·0x2dede5d0>

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·0x~~354d~~f380>,·<FrictPhys·instance·at·0x37e1~~d95~~0>)	572	Out[30]:·(<ScGeom·instance·at·0x2de2ef30>,·<FrictPhys·instance·at·0x2e18f000>)
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@ionos5-amd64)',	917	{'author':·'second~user~(pbuilder2@i-capture-the-hostname)',
918	·'isoTime':·'20260~~830~~T001552',	918	·'isoTime':·'20250729T101842',
919	·'id':·'20260830T001552p3203197',
920	·'d.id':·'20260830T001552p3203197',
921	·'id.d':·'20260~~830~~T001552p320~~3197~~'}	919	·'id':·'20250729T101842p205626',
		920	·'d.id':·'20250729T101842p205626',
		921	·'id.d':·'20250729T101842p205626'}
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·0x7f2005867380>,	1585	{'sand':·<yade.utils.YadeColorStyle·at·0x7f04c836f380>,
1586	·'old':·<yade.utils.YadeColorStyle·at·0x7f20058d1a90>,	1586	·'old':·<yade.utils.YadeColorStyle·at·0x7f04c83d5a90>,
1587	·'figureColor':·<yade.utils.YadeColorStyle·at·0x7f20058d1bd0>,	1587	·'figureColor':·<yade.utils.YadeColorStyle·at·0x7f04c83d5bd0>,
1588	·'figureGrey':·<yade.utils.YadeColorStyle·at·0x7f20058f8050>,	1588	·'figureGrey':·<yade.utils.YadeColorStyle·at·0x7f04c83f8050>,
1589	·'blue':·<yade.utils.YadeColorStyle·at·0x7f20058f82b0>,	1589	·'blue':·<yade.utils.YadeColorStyle·at·0x7f04c83f82b0>,
1590	·'screenDisplayLowRes':·<yade.utils.YadeColorStyle·at·0x7f2005886690>}	1590	·'screenDisplayLowRes':·<yade.utils.YadeColorStyle·at·0x7f04c838a690>}
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 36588, 15 lines modified		Offset 36588, 15 lines modified
36588	<dt·class="sig·sig-object·py"·id="yade.plot.Subdomain.completeSendBodies">	36588	<dt·class="sig·sig-object·py"·id="yade.plot.Subdomain.completeSendBodies">
36589	<span·class="sig-name·descname"><span·class="pre">completeSendBodies</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(Subdomain)arg1</span></span></em><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><span·class="pre">None</span>·<span·class="pre">:</span></span></span><a·class="headerlink"·href="#yade.plot.Subdomain.completeSendBodies"·title="Link·to·this·definition">¶</a></dt>	36589	<span·class="sig-name·descname"><span·class="pre">completeSendBodies</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(Subdomain)arg1</span></span></em><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><span·class="pre">None</span>·<span·class="pre">:</span></span></span><a·class="headerlink"·href="#yade.plot.Subdomain.completeSendBodies"·title="Link·to·this·definition">¶</a></dt>
36590	<dd><p>calls·MPI_wait·to·complete·the·non·blocking·sends/recieves.</p>	36590	<dd><p>calls·MPI_wait·to·complete·the·non·blocking·sends/recieves.</p>
36591	</dd></dl>	36591	</dd></dl>

36592	<dl·class="py·method">	36592	<dl·class="py·method">
36593	<dt·class="sig·sig-object·py"·id="yade.plot.Subdomain.countIntsWith">	36593	<dt·class="sig·sig-object·py"·id="yade.plot.Subdomain.countIntsWith">
36594	<span·class="sig-name·descname"><span·class="pre">countIntsWith</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(Subdomain)arg1</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">(int)body</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">(int)someSubDomain</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(Scene)someSubDomain=<Scene</span>·<span·class="pre">instance</span>·<span·class="pre">at</span>·<span·class="pre">0x~~354ddcb~~0></span></span></em><span·class="optional">]</span><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><span·class="pre">int</span>·<span·class="pre">:</span></span></span><a·class="headerlink"·href="#yade.plot.Subdomain.countIntsWith"·title="Link·to·this·definition">¶</a></dt>	36594	<span·class="sig-name·descname"><span·class="pre">countIntsWith</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(Subdomain)arg1</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">(int)body</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">(int)someSubDomain</span></span></em><span·class="optional">[</span>,·<em·class="sig-param"><span·class="n"><span·class="pre">(Scene)someSubDomain=<Scene</span>·<span·class="pre">instance</span>·<span·class="pre">at</span>·<span·class="pre">0x2b576960></span></span></em><span·class="optional">]</span><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><span·class="pre">int</span>·<span·class="pre">:</span></span></span><a·class="headerlink"·href="#yade.plot.Subdomain.countIntsWith"·title="Link·to·this·definition">¶</a></dt>
36595	<dd><p>returns·for·a·body·the·count·of·interactions·(real·or·virtual)·with·bodies·from·a·certain·subdomain,·interactions·with·subdomains·excluded.·Third·parameter·(scene·pointer)·can·be·left·to·default·(equivalent·to·O._sceneObj).</p>	36595	<dd><p>returns·for·a·body·the·count·of·interactions·(real·or·virtual)·with·bodies·from·a·certain·subdomain,·interactions·with·subdomains·excluded.·Third·parameter·(scene·pointer)·can·be·left·to·default·(equivalent·to·O._sceneObj).</p>
36596	</dd></dl>	36596	</dd></dl>

36597	<dl·class="py·method">	36597	<dl·class="py·method">
36598	<dt·class="sig·sig-object·py"·id="yade.plot.Subdomain.dict">	36598	<dt·class="sig·sig-object·py"·id="yade.plot.Subdomain.dict">
36599	<span·class="sig-name·descname"><span·class="pre">dict</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(Serializable)arg1</span></span></em><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><span·class="pre">dict</span>·<span·class="pre">:</span></span></span><a·class="headerlink"·href="#yade.plot.Subdomain.dict"·title="Link·to·this·definition">¶</a></dt>	36599	<span·class="sig-name·descname"><span·class="pre">dict</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">(Serializable)arg1</span></span></em><span·class="sig-paren">)</span>·<span·class="sig-return"><span·class="sig-return-icon">→</span>·<span·class="sig-return-typehint"><span·class="pre">dict</span>·<span·class="pre">:</span></span></span><a·class="headerlink"·href="#yade.plot.Subdomain.dict"·title="Link·to·this·definition">¶</a></dt>
36600	<dd><p>Return·dictionary·of·attributes.</p>	36600	<dd><p>Return·dictionary·of·attributes.</p>


Offset 17539, 15 lines modified		Offset 17539, 15 lines modified
17539	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶	17539	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶
17540	············Color·for·rendering·(normalized·RGB).	17540	············Color·for·rendering·(normalized·RGB).
17541	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·comm_\x8¶	17541	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·comm_\x8¶
17542	············Communicator·to·be·used·for·MPI·(converts·mpi4py·comm·<->·c++·comm)	17542	············Communicator·to·be·used·for·MPI·(converts·mpi4py·comm·<->·c++·comm)
17543	········completeSendBodies((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81)·→·None·:_\x8¶	17543	········completeSendBodies((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81)·→·None·:_\x8¶
17544	············calls·MPI_wait·to·complete·the·non·blocking·sends/recieves.	17544	············calls·MPI_wait·to·complete·the·non·blocking·sends/recieves.
17545	········countIntsWith((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81,·(\x8(i\x8in\x8nt\x8t)\x8)b\x8bo\x8od\x8dy\x8y,·(\x8(i\x8in\x8nt\x8t)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n[,	17545	········countIntsWith((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81,·(\x8(i\x8in\x8nt\x8t)\x8)b\x8bo\x8od\x8dy\x8y,·(\x8(i\x8in\x8nt\x8t)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n[,
17546	········(\x8(S\x8Sc\x8ce\x8en\x8ne\x8e)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n=\x8=<\x8<S\x8Sc\x8ce\x8en\x8ne\x8e·i\x8in\x8ns\x8st\x8ta\x8an\x8nc\x8ce\x8e·a\x8at\x8t·0\x80x\x8x3.35.54.4d.dd.dc.cb.b0\x80>\x8>])·→·int·:_\x8¶	17546	········(\x8(S\x8Sc\x8ce\x8en\x8ne\x8e)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n=\x8=<\x8<S\x8Sc\x8ce\x8en\x8ne\x8e·i\x8in\x8ns\x8st\x8ta\x8an\x8nc\x8ce\x8e·a\x8at\x8t·0\x80x\x8x2.2b.b5.57.76.69.96.60\x80>\x8>])·→·int·:_\x8¶
17547	············returns·for·a·body·the·count·of·interactions·(real·or·virtual)·with	17547	············returns·for·a·body·the·count·of·interactions·(real·or·virtual)·with
17548	············bodies·from·a·certain·subdomain,·interactions·with·subdomains	17548	············bodies·from·a·certain·subdomain,·interactions·with·subdomains
17549	············excluded.·Third·parameter·(scene·pointer)·can·be·left·to·default	17549	············excluded.·Third·parameter·(scene·pointer)·can·be·left·to·default
17550	············(equivalent·to·O._sceneObj).	17550	············(equivalent·to·O._sceneObj).
17551	········dict((\x8(S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)\x8)a\x8ar\x8rg\x8g1\x81)·→·dict·:_\x8¶	17551	········dict((\x8(S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)\x8)a\x8ar\x8rg\x8g1\x81)·→·dict·:_\x8¶
17552	············Return·dictionary·of·attributes.	17552	············Return·dictionary·of·attributes.
17553	········dispHierarchy((\x8(S\x8Sh\x8ha\x8ap\x8pe\x8e)\x8)a\x8ar\x8rg\x8g1\x81[,·(\x8(b\x8bo\x8oo\x8ol\x8l)\x8)n\x8na\x8am\x8me\x8es\x8s=\x8=T\x8Tr\x8ru\x8ue\x8e])·→·list·:_\x8¶	17553	········dispHierarchy((\x8(S\x8Sh\x8ha\x8ap\x8pe\x8e)\x8)a\x8ar\x8rg\x8g1\x81[,·(\x8(b\x8bo\x8oo\x8ol\x8l)\x8)n\x8na\x8am\x8me\x8es\x8s=\x8=T\x8Tr\x8ru\x8ue\x8e])·→·list·:_\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">0x361~~f615~~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">0x2c12f330></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\x8x3.36.61.1f.f6.61.15.50\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\x8x2.2c.c1.12.2f.f3.33.30\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 113, 81 lines modified		Offset 113, 81 lines modified
113	············Update·object·attributes·from·given·dictionary	113	············Update·object·attributes·from·given·dictionary
114	\x8\x8\x8\x8·S\x8Sh\x8ha\x8ap\x8pe\x8e_\x8?\x8¶·\x8\x8\x8\x8	114	\x8\x8\x8\x8·S\x8Sh\x8ha\x8ap\x8pe\x8e_\x8?\x8¶·\x8\x8\x8\x8
115	[digraph·Shape·{	115	[digraph·Shape·{
116	········rankdir=RL;	116	········rankdir=RL;
117	········margin="0.2,0.05";	117	········margin="0.2,0.05";
118	········"Shape"·[shape="box",fontsize=8,style="setlinewidth	118	········"Shape"·[shape="box",fontsize=8,style="setlinewidth
119	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Shape"];	119	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Shape"];
120	········"PFacet"·[shape="box",fontsize=8,style="setlinewidth
121	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
122	········"PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
123	········"Node"·[shape="box",fontsize=8,style="setlinewidth	120	········"Cylinder"·[shape="box",fontsize=8,style="setlinewidth
124	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];	121	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
125	········"Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	122	········"Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		123	········"PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth
		124	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
		125	········"PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
		126	(0.5)"];
126	········"GridNode"·[shape="box",fontsize=8,style="setlinewidth	127	········"GridNode"·[shape="box",fontsize=8,style="setlinewidth
127	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];	128	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridNode"];
128	········"GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	129	········"GridNode"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
129	········"LevelSet"·[shape="box",fontsize=8,style="setlinewidth	130	········"DeformableElement"·[shape="box",fontsize=8,style="setlinewidth
130	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];	131	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];
		132	········"DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
		133	(0.5)"];
		134	········"GridConnection"·[shape="box",fontsize=8,style="setlinewidth
		135	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.GridConnection"];
131	········"~~LevelS~~et"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	136	········"GridConnection"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
132	········"DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth	137	········"DeformableCohesiveElement"·[shape="box",fontsize=8,style="setlinewidth
133	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];	138	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableCohesiveElement"];
134	········"DeformableCohesiveElement"·->·"DeformableElement"	139	········"DeformableCohesiveElement"·->·"DeformableElement"
135	[arrowsize=0.5,style="setlinewidth(0.5)"];	140	[arrowsize=0.5,style="setlinewidth(0.5)"];
136	········"Sphere"·[shape="box",fontsize=8,style="setlinewidth
137	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
138	········"Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
139	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"
140	[shape="box",fontsize=8,style="setlinewidth
141	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
142	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·-
143	>·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
144	········"Tetra"·[shape="box",fontsize=8,style="setlinewidth
145	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];
146	········"Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
147	········"Cylinder"·[shape="box",fontsize=8,style="setlinewidth
148	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Cylinder"];
149	········"Cylinder"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];
150	········"Wall"·[shape="box",fontsize=8,style="setlinewidth	141	········"Wall"·[shape="box",fontsize=8,style="setlinewidth
151	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];	142	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Wall"];
152	········"Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	143	········"Wall"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
153	········"ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth
154	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];
155	········"ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth
156	(0.5)"];
157	········"~~Clump~~"·[shape="box",fontsize=8,style="setlinewidth	144	········"Facet"·[shape="box",fontsize=8,style="setlinewidth
158	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.~~Clump~~"];	145	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
159	········"~~Clump~~"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	146	········"Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		147	········"PFacet"·[shape="box",fontsize=8,style="setlinewidth
		148	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PFacet"];
		149	········"PFacet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
160	········"Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth	150	········"Lin4NodeTetra"·[shape="box",fontsize=8,style="setlinewidth
161	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];	151	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra"];
162	········"Lin4NodeTetra"·->·"DeformableElement"	152	········"Lin4NodeTetra"·->·"DeformableElement"
163	[arrowsize=0.5,style="setlinewidth(0.5)"];	153	[arrowsize=0.5,style="setlinewidth(0.5)"];
164	········"Facet"·[shape="box",fontsize=8,style="setlinewidth
165	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Facet"];
166	········"Facet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
167	········"DeformableElement"·[shape="box",fontsize=8,style="setlinewidth
168	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.DeformableElement"];
169	········"DeformableElement"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
170	(0.5)"];
171	········"Subdomain"·[shape="box",fontsize=8,style="setlinewidth
172	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Subdomain"];
173	········"Subdomain"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
174	········"PotentialParticle"·[shape="box",fontsize=8,style="setlinewidth
175	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.PotentialParticle"];
176	········"PotentialParticle"·->·"Shape"·[arrowsize=0.5,style="setlinewidth
177	(0.5)"];
178	········"FluidDomainBbox"·[shape="box",fontsize=8,style="setlinewidth	154	········"FluidDomainBbox"·[shape="box",fontsize=8,style="setlinewidth
179	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FluidDomainBbox"];	155	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.FluidDomainBbox"];
180	········"FluidDomainBbox"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	156	········"FluidDomainBbox"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		157	········"ChainedCylinder"·[shape="box",fontsize=8,style="setlinewidth
		158	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.ChainedCylinder"];
		159	········"ChainedCylinder"·->·"Cylinder"·[arrowsize=0.5,style="setlinewidth
		160	(0.5)"];
		161	········"Sphere"·[shape="box",fontsize=8,style="setlinewidth
		162	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Sphere"];
		163	········"Sphere"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		164	········"Clump"·[shape="box",fontsize=8,style="setlinewidth
		165	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Clump"];
		166	········"Clump"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
181	········"Box"·[shape="box",fontsize=8,style="setlinewidth	167	········"Box"·[shape="box",fontsize=8,style="setlinewidth
182	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];	168	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Box"];
183	········"Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];	169	········"Box"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		170	········"Subdomain"·[shape="box",fontsize=8,style="setlinewidth
		171	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Subdomain"];
		172	········"Subdomain"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
184	········"~~Grid~~Conne~~ction~~"·[shape="box",fontsize=8,style="setlinewidth	173	········"Node"·[shape="box",fontsize=8,style="setlinewidth
185	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.~~Grid~~Conne~~ction~~"];	174	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Node"];
186	········"~~Grid~~Conne~~ction~~"·->·"Sphere"·[arrowsize=0.5,style="setlinewidth(0.5)"];	175	········"Node"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		176	········"LevelSet"·[shape="box",fontsize=8,style="setlinewidth
		177	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.LevelSet"];
		178	········"LevelSet"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		179	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"
		180	[shape="box",fontsize=8,style="setlinewidth
		181	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Lin4NodeTetra_Lin4NodeTetra_InteractionElement"];
		182	········"Lin4NodeTetra_Lin4NodeTetra_InteractionElement"·-
		183	>·"DeformableCohesiveElement"·[arrowsize=0.5,style="setlinewidth(0.5)"];
		184	········"Tetra"·[shape="box",fontsize=8,style="setlinewidth
		185	(0.5),solid",height=0.2,URL="yade.wrapper.html#yade.wrapper.Tetra"];
		186	········"Tetra"·->·"Shape"·[arrowsize=0.5,style="setlinewidth(0.5)"];
187	}]	187	}]
188	Inheritance·graph·of·Shape._\x8¶	188	Inheritance·graph·of·Shape._\x8¶
189	··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¶	189	··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¶
190	······Geometry·of·a·body	190	······Geometry·of·a·body
191	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶	191	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶
192	············Color·for·rendering·(normalized·RGB).	192	············Color·for·rendering·(normalized·RGB).
193	········dict((\x8(S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)\x8)a\x8ar\x8rg\x8g1\x81)·→·dict·:_\x8¶	193	········dict((\x8(S\x8Se\x8er\x8ri\x8ia\x8al\x8li\x8iz\x8za\x8ab\x8bl\x8le\x8e)\x8)a\x8ar\x8rg\x8g1\x81)·→·dict·:_\x8¶
Offset 921, 15 lines modified		Offset 921, 15 lines modified
921	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶	921	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·color_\x8¶
922	············Color·for·rendering·(normalized·RGB).	922	············Color·for·rendering·(normalized·RGB).
923	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·comm_\x8¶	923	········p\x8pr\x8ro\x8op\x8pe\x8er\x8rt\x8ty\x8y·comm_\x8¶
924	············Communicator·to·be·used·for·MPI·(converts·mpi4py·comm·<->·c++·comm)	924	············Communicator·to·be·used·for·MPI·(converts·mpi4py·comm·<->·c++·comm)
925	········completeSendBodies((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81)·→·None·:_\x8¶	925	········completeSendBodies((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81)·→·None·:_\x8¶
926	············calls·MPI_wait·to·complete·the·non·blocking·sends/recieves.	926	············calls·MPI_wait·to·complete·the·non·blocking·sends/recieves.
927	········countIntsWith((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81,·(\x8(i\x8in\x8nt\x8t)\x8)b\x8bo\x8od\x8dy\x8y,·(\x8(i\x8in\x8nt\x8t)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n[,	927	········countIntsWith((\x8(S\x8Su\x8ub\x8bd\x8do\x8om\x8ma\x8ai\x8in\x8n)\x8)a\x8ar\x8rg\x8g1\x81,·(\x8(i\x8in\x8nt\x8t)\x8)b\x8bo\x8od\x8dy\x8y,·(\x8(i\x8in\x8nt\x8t)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n[,
928	········(\x8(S\x8Sc\x8ce\x8en\x8ne\x8e)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n=\x8=<\x8<S\x8Sc\x8ce\x8en\x8ne\x8e·i\x8in\x8ns\x8st\x8ta\x8an\x8nc\x8ce\x8e·a\x8at\x8t·0\x80x\x8x3.35.54.4d.dd.dc.cb.b0\x80>\x8>])·→·int·:_\x8¶	928	········(\x8(S\x8Sc\x8ce\x8en\x8ne\x8e)\x8)s\x8so\x8om\x8me\x8eS\x8Su\x8ub\x8bD\x8Do\x8om\x8ma\x8ai\x8in\x8n=\x8=<\x8<S\x8Sc\x8ce\x8en\x8ne\x8e·i\x8in\x8ns\x8st\x8ta\x8an\x8nc\x8ce\x8e·a\x8at\x8t·0\x80x\x8x2.2b.b5.57.76.69.96.60\x80>\x8>])·→·int·:_\x8¶
929	············returns·for·a·body·the·count·of·interactions·(real·or·virtual)·with	929	············returns·for·a·body·the·count·of·interactions·(real·or·virtual)·with
930	············bodies·from·a·certain·subdomain,·interactions·with·subdomains	930	············bodies·from·a·certain·subdomain,·interactions·with·subdomains
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Offset 1, 17 lines modified		Offset 1, 17 lines modified
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Offset 1, 8 lines modified		Offset 1, 8 lines modified
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Offset 1, 13 lines modified		Offset 1, 13 lines modified
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Offset 1, 34 lines modified		Offset 1, 34 lines modified
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Offset 1, 18 lines modified		Offset 1, 18 lines modified
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