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NonConvexEnvelope.r3d@ eaef9b

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Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 Candidate_v1.7.0 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion GeometryObjects Gui_displays_atomic_force_velocity IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks RotateToPrincipalAxisSystem_UndoRedo StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps Ubuntu_1604_changes stable

Last change on this file since eaef9b was 560bbe, checked in by Frederik Heber <heber@…>, 14 years ago

AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own IdPool.

molecule now also has an internal IdPool to be able to hand out unique ids, according to uniqueId policy.
new functions: molecule::changeAtomNr(), molecule::setAtomName()
molecule::erase() and ::insert() release and set the id (and the name).
molecule::setAtomName() uses getNr() with id increased by one.
AtomicInfo stores and sets ParticleInfo::Nr.
atom::changeNr() is similar to changeId() only for the molecule.
molecule::AddAtom() does not set the name anymore, is done by ::insert().
simplified molecule::doCountAtoms() a lot, no more naming of atoms.
SPEEDUP: This speeds up the GUI already a lot.
TESTFIX: changed regression test Tesselation/BigNonConvex due to different ordering of node ids (due to above), surface is still the same (checked).

Property mode set to 100644

File size: 11.6 KB

Line
1	# Raster3D object description, created by MoleCuilder
2	@header.r3d
3	# All atoms as spheres
4	2
5	0.777562 -3.65286 1.28459 0.1 1. 1. 1.
6	2
7	0.904762 -3.62316 -0.490507 0.1 1. 1. 1.
8	2
9	1.91486 -2.53606 0.492393 0.1 1. 1. 1.
10	2
11	-0.587138 -0.162455 -0.830407 0.1 1. 1. 1.
12	2
13	-1.53704 -3.60006 0.497793 0.1 1. 1. 1.
14	2
15	-0.771938 -0.223855 1.47919 0.1 1. 1. 1.
16	2
17	-0.300138 -1.62946 2.47449 0.1 1. 1. 1.
18	2
19	2.17906 -1.47276 -0.873307 0.1 1. 1. 1.
20	2
21	-0.586638 -1.38326 -2.92321 0.1 1. 1. 1.
22	2
23	0.438062 -2.68776 -2.23921 0.1 1. 1. 1.
24	2
25	-2.47214 -1.59546 1.71589 0.1 1. 1. 1.
26	2
27	-1.64154 -3.70136 -1.80061 0.1 1. 1. 1.
28	2
29	-2.50954 -2.13946 -1.80561 0.1 1. 1. 1.
30	2
31	1.45166 0.153645 2.50359 0.1 1. 1. 1.
32	2
33	2.04886 -1.35716 1.79219 0.1 1. 1. 1.
34	2
35	1.14346 1.15214 0.320993 0.1 1. 1. 1.
36	2
37	1.75376 -0.319055 -2.99941 0.1 1. 1. 1.
38	2
39	1.01996 1.06104 -2.15101 0.1 1. 1. 1.
40	2
41	-1.71014 0.133845 0.126293 0.1 1. 1. 1.
42	2
43	-2.78704 -0.528955 -1.12651 0.1 1. 1. 1.
44	2
45	-4.76454 -1.89276 0.930293 0.1 1. 1. 1.
46	2
47	-4.18614 -2.49696 -0.640907 0.1 1. 1. 1.
48	2
49	-3.92214 -3.45776 0.834093 0.1 1. 1. 1.
50	2
51	3.60736 1.29684 -2.87381 0.1 1. 1. 1.
52	2
53	-4.75094 -0.0564554 0.311693 0.1 1. 1. 1.
54	2
55	-3.67414 0.606345 1.56439 0.1 1. 1. 1.
56	2
57	3.22946 1.45274 2.47189 0.1 1. 1. 1.
58	2
59	4.33006 2.26874 1.33549 0.1 1. 1. 1.
60	2
61	2.57536 2.54894 1.23139 0.1 1. 1. 1.
62	2
63	4.07696 -0.484155 2.10119 0.1 1. 1. 1.
64	2
65	3.61706 -1.46676 0.692693 0.1 1. 1. 1.
66	2
67	-2.88384 2.33404 -0.0290068 0.1 1. 1. 1.
68	2
69	-3.96064 1.67134 -1.28171 0.1 1. 1. 1.
70	2
71	5.67566 1.42984 -1.78291 0.1 1. 1. 1.
72	2
73	5.10266 2.74254 -0.715907 0.1 1. 1. 1.
74	2
75	6.16236 -0.927955 1.16559 0.1 1. 1. 1.
76	2
77	5.53756 -0.911555 -0.496607 0.1 1. 1. 1.
78	2
79	-4.84774 2.80654 1.40919 0.1 1. 1. 1.
80	2
81	5.68906 1.58194 1.24439 0.1 1. 1. 1.
82	2
83	-5.82304 4.61784 0.0247932 0.1 1. 1. 1.
84	2
85	-4.05744 4.53424 -0.184207 0.1 1. 1. 1.
86	2
87	-5.13424 3.87154 -1.43691 0.1 1. 1. 1.
88	2
89	-6.29174 0.967445 0.583993 0.1 1. 1. 1.
90	2
91	-7.12784 2.53484 0.473393 0.1 1. 1. 1.
92	2
93	-6.43904 1.78854 -0.988307 0.1 1. 1. 1.
94	2
95	7.55546 2.01984 -0.0120068 0.1 1. 1. 1.
96	2
97	0.939662 -3.01666 0.414493 0.1 1. 1. 1.
98	2
99	-0.152738 -1.94716 0.354093 0.1 1. 1. 1.
100	2
101	0.0659622 -1.03376 -0.880907 0.1 1. 1. 1.
102	2
103	-1.50434 -2.59696 0.0723932 0.1 1. 1. 1.
104	2
105	-0.0717378 -1.05346 1.57779 0.1 1. 1. 1.
106	2
107	1.52186 -0.603155 -0.873807 0.1 1. 1. 1.
108	2
109	-0.346038 -1.95996 -2.03011 0.1 1. 1. 1.
110	2
111	-2.63434 -1.74086 0.647893 0.1 1. 1. 1.
112	2
113	-1.61364 -2.66266 -1.47131 0.1 1. 1. 1.
114	2
115	1.36626 -0.519255 1.65039 0.1 1. 1. 1.
116	2
117	1.74646 0.246745 0.389693 0.1 1. 1. 1.
118	2
119	1.78606 0.287745 -2.09451 0.1 1. 1. 1.
120	2
121	-2.65324 -0.381955 -0.0548068 0.1 1. 1. 1.
122	2
123	-3.97304 -2.44796 0.426993 0.1 1. 1. 1.
124	2
125	3.21726 0.635145 0.478793 0.1 1. 1. 1.
126	2
127	3.13516 0.931145 -1.97401 0.1 1. 1. 1.
128	2
129	-3.80794 0.459345 0.492693 0.1 1. 1. 1.
130	2
131	3.34736 1.81094 1.44919 0.1 1. 1. 1.
132	2
133	3.76986 1.05884 -0.855107 0.1 1. 1. 1.
134	2
135	4.05806 -0.522555 1.01199 0.1 1. 1. 1.
136	2
137	-3.82684 1.81824 -0.210007 0.1 1. 1. 1.
138	2
139	5.16496 1.66244 -0.848507 0.1 1. 1. 1.
140	2
141	5.48576 -0.422855 0.476393 0.1 1. 1. 1.
142	2
143	-4.98154 2.65954 0.337493 0.1 1. 1. 1.
144	2
145	5.91796 1.03174 0.331693 0.1 1. 1. 1.
146	2
147	-5.00044 4.01854 -0.365207 0.1 1. 1. 1.
148	2
149	-6.30524 1.93554 0.0833932 0.1 1. 1. 1.
150	2
151	7.32406 1.08574 0.0829932 0.1 1. 1. 1.
152	# All tesselation triangles
153	8
154	25. -1. 1. 1. 1. 0.0 0 0 0 2
155	SOLID 1.0 0.0 0.0
156	BACKFACE 0.3 0.3 1.0 0 0
157	1
158	7.32406 1.08574 0.0829932 5.67566 1.42984 -1.78291 7.55546 2.01984 -0.0120068 1. 0. 0.
159	1
160	7.32406 1.08574 0.0829932 5.67566 1.42984 -1.78291 5.53756 -0.911555 -0.496607 1. 0. 0.
161	1
162	7.32406 1.08574 0.0829932 6.16236 -0.927955 1.16559 5.53756 -0.911555 -0.496607 1. 0. 0.
163	1
164	3.60736 1.29684 -2.87381 5.67566 1.42984 -1.78291 5.53756 -0.911555 -0.496607 1. 0. 0.
165	1
166	1.75376 -0.319055 -2.99941 3.60736 1.29684 -2.87381 5.53756 -0.911555 -0.496607 1. 0. 0.
167	1
168	2.17906 -1.47276 -0.873307 1.75376 -0.319055 -2.99941 5.53756 -0.911555 -0.496607 1. 0. 0.
169	1
170	2.17906 -1.47276 -0.873307 0.438062 -2.68776 -2.23921 1.75376 -0.319055 -2.99941 1. 0. 0.
171	1
172	0.904762 -3.62316 -0.490507 2.17906 -1.47276 -0.873307 0.438062 -2.68776 -2.23921 1. 0. 0.
173	1
174	0.904762 -3.62316 -0.490507 2.17906 -1.47276 -0.873307 5.53756 -0.911555 -0.496607 1. 0. 0.
175	1
176	0.904762 -3.62316 -0.490507 1.91486 -2.53606 0.492393 5.53756 -0.911555 -0.496607 1. 0. 0.
177	1
178	1.91486 -2.53606 0.492393 3.61706 -1.46676 0.692693 5.53756 -0.911555 -0.496607 1. 0. 0.
179	1
180	3.61706 -1.46676 0.692693 6.16236 -0.927955 1.16559 5.53756 -0.911555 -0.496607 1. 0. 0.
181	1
182	0.777562 -3.65286 1.28459 0.904762 -3.62316 -0.490507 1.91486 -2.53606 0.492393 1. 0. 0.
183	1
184	0.777562 -3.65286 1.28459 1.91486 -2.53606 0.492393 3.61706 -1.46676 0.692693 1. 0. 0.
185	1
186	0.777562 -3.65286 1.28459 2.04886 -1.35716 1.79219 3.61706 -1.46676 0.692693 1. 0. 0.
187	1
188	2.04886 -1.35716 1.79219 4.07696 -0.484155 2.10119 3.61706 -1.46676 0.692693 1. 0. 0.
189	1
190	4.07696 -0.484155 2.10119 3.61706 -1.46676 0.692693 6.16236 -0.927955 1.16559 1. 0. 0.
191	1
192	0.777562 -3.65286 1.28459 -0.300138 -1.62946 2.47449 2.04886 -1.35716 1.79219 1. 0. 0.
193	1
194	-0.300138 -1.62946 2.47449 1.45166 0.153645 2.50359 2.04886 -1.35716 1.79219 1. 0. 0.
195	1
196	1.45166 0.153645 2.50359 2.04886 -1.35716 1.79219 4.07696 -0.484155 2.10119 1. 0. 0.
197	1
198	1.45166 0.153645 2.50359 3.22946 1.45274 2.47189 4.07696 -0.484155 2.10119 1. 0. 0.
199	1
200	3.22946 1.45274 2.47189 4.07696 -0.484155 2.10119 5.68906 1.58194 1.24439 1. 0. 0.
201	1
202	4.07696 -0.484155 2.10119 6.16236 -0.927955 1.16559 5.68906 1.58194 1.24439 1. 0. 0.
203	1
204	7.32406 1.08574 0.0829932 6.16236 -0.927955 1.16559 5.68906 1.58194 1.24439 1. 0. 0.
205	1
206	7.32406 1.08574 0.0829932 5.68906 1.58194 1.24439 7.55546 2.01984 -0.0120068 1. 0. 0.
207	1
208	3.22946 1.45274 2.47189 4.33006 2.26874 1.33549 5.68906 1.58194 1.24439 1. 0. 0.
209	1
210	3.22946 1.45274 2.47189 4.33006 2.26874 1.33549 2.57536 2.54894 1.23139 1. 0. 0.
211	1
212	4.33006 2.26874 1.33549 2.57536 2.54894 1.23139 5.10266 2.74254 -0.715907 1. 0. 0.
213	1
214	4.33006 2.26874 1.33549 5.10266 2.74254 -0.715907 7.55546 2.01984 -0.0120068 1. 0. 0.
215	1
216	4.33006 2.26874 1.33549 5.68906 1.58194 1.24439 7.55546 2.01984 -0.0120068 1. 0. 0.
217	1
218	1.45166 0.153645 2.50359 3.22946 1.45274 2.47189 2.57536 2.54894 1.23139 1. 0. 0.
219	1
220	1.45166 0.153645 2.50359 2.57536 2.54894 1.23139 -2.88384 2.33404 -0.0290068 1. 0. 0.
221	1
222	-0.771938 -0.223855 1.47919 1.45166 0.153645 2.50359 -2.88384 2.33404 -0.0290068 1. 0. 0.
223	1
224	-0.771938 -0.223855 1.47919 -3.67414 0.606345 1.56439 -2.88384 2.33404 -0.0290068 1. 0. 0.
225	1
226	-3.67414 0.606345 1.56439 -2.88384 2.33404 -0.0290068 -4.84774 2.80654 1.40919 1. 0. 0.
227	1
228	-2.88384 2.33404 -0.0290068 -4.84774 2.80654 1.40919 -4.05744 4.53424 -0.184207 1. 0. 0.
229	1
230	2.57536 2.54894 1.23139 -2.88384 2.33404 -0.0290068 -4.05744 4.53424 -0.184207 1. 0. 0.
231	1
232	2.57536 2.54894 1.23139 -2.88384 2.33404 -0.0290068 -4.05744 4.53424 -0.184207 1. 0. 0.
233	1
234	1.14346 1.15214 0.320993 2.57536 2.54894 1.23139 -2.88384 2.33404 -0.0290068 1. 0. 0.
235	1
236	1.14346 1.15214 0.320993 1.01996 1.06104 -2.15101 -2.88384 2.33404 -0.0290068 1. 0. 0.
237	1
238	1.14346 1.15214 0.320993 1.01996 1.06104 -2.15101 2.57536 2.54894 1.23139 1. 0. 0.
239	1
240	1.01996 1.06104 -2.15101 2.57536 2.54894 1.23139 5.10266 2.74254 -0.715907 1. 0. 0.
241	1
242	1.01996 1.06104 -2.15101 3.60736 1.29684 -2.87381 5.10266 2.74254 -0.715907 1. 0. 0.
243	1
244	-0.771938 -0.223855 1.47919 -0.300138 -1.62946 2.47449 -3.67414 0.606345 1.56439 1. 0. 0.
245	1
246	-0.771938 -0.223855 1.47919 -0.300138 -1.62946 2.47449 1.45166 0.153645 2.50359 1. 0. 0.
247	1
248	-0.300138 -1.62946 2.47449 -2.47214 -1.59546 1.71589 -3.67414 0.606345 1.56439 1. 0. 0.
249	1
250	-2.47214 -1.59546 1.71589 -4.76454 -1.89276 0.930293 -3.67414 0.606345 1.56439 1. 0. 0.
251	1
252	-4.76454 -1.89276 0.930293 -3.67414 0.606345 1.56439 -6.29174 0.967445 0.583993 1. 0. 0.
253	1
254	-3.67414 0.606345 1.56439 -4.84774 2.80654 1.40919 -6.29174 0.967445 0.583993 1. 0. 0.
255	1
256	-4.84774 2.80654 1.40919 -6.29174 0.967445 0.583993 -7.12784 2.53484 0.473393 1. 0. 0.
257	1
258	-2.47214 -1.59546 1.71589 -4.76454 -1.89276 0.930293 -3.92214 -3.45776 0.834093 1. 0. 0.
259	1
260	-1.53704 -3.60006 0.497793 -2.47214 -1.59546 1.71589 -3.92214 -3.45776 0.834093 1. 0. 0.
261	1
262	-1.53704 -3.60006 0.497793 -0.300138 -1.62946 2.47449 -2.47214 -1.59546 1.71589 1. 0. 0.
263	1
264	0.777562 -3.65286 1.28459 -1.53704 -3.60006 0.497793 -0.300138 -1.62946 2.47449 1. 0. 0.
265	1
266	-4.84774 2.80654 1.40919 -5.82304 4.61784 0.0247932 -4.05744 4.53424 -0.184207 1. 0. 0.
267	1
268	-4.84774 2.80654 1.40919 -5.82304 4.61784 0.0247932 -7.12784 2.53484 0.473393 1. 0. 0.
269	1
270	1.01996 1.06104 -2.15101 -2.88384 2.33404 -0.0290068 -3.96064 1.67134 -1.28171 1. 0. 0.
271	1
272	-2.88384 2.33404 -0.0290068 -3.96064 1.67134 -1.28171 -4.05744 4.53424 -0.184207 1. 0. 0.
273	1
274	-3.96064 1.67134 -1.28171 -4.05744 4.53424 -0.184207 -5.13424 3.87154 -1.43691 1. 0. 0.
275	1
276	-0.586638 -1.38326 -2.92321 1.01996 1.06104 -2.15101 -3.96064 1.67134 -1.28171 1. 0. 0.
277	1
278	-0.586638 -1.38326 -2.92321 1.75376 -0.319055 -2.99941 1.01996 1.06104 -2.15101 1. 0. 0.
279	1
280	1.75376 -0.319055 -2.99941 1.01996 1.06104 -2.15101 3.60736 1.29684 -2.87381 1. 0. 0.
281	1
282	-0.586638 -1.38326 -2.92321 -2.78704 -0.528955 -1.12651 -3.96064 1.67134 -1.28171 1. 0. 0.
283	1
284	-0.586638 -1.38326 -2.92321 -2.50954 -2.13946 -1.80561 -2.78704 -0.528955 -1.12651 1. 0. 0.
285	1
286	-2.50954 -2.13946 -1.80561 -2.78704 -0.528955 -1.12651 -3.96064 1.67134 -1.28171 1. 0. 0.
287	1
288	-2.50954 -2.13946 -1.80561 -4.18614 -2.49696 -0.640907 -3.96064 1.67134 -1.28171 1. 0. 0.
289	1
290	-4.18614 -2.49696 -0.640907 -3.96064 1.67134 -1.28171 -6.43904 1.78854 -0.988307 1. 0. 0.
291	1
292	-3.96064 1.67134 -1.28171 -5.13424 3.87154 -1.43691 -6.43904 1.78854 -0.988307 1. 0. 0.
293	1
294	-0.586638 -1.38326 -2.92321 -1.64154 -3.70136 -1.80061 -2.50954 -2.13946 -1.80561 1. 0. 0.
295	1
296	-0.586638 -1.38326 -2.92321 0.438062 -2.68776 -2.23921 -1.64154 -3.70136 -1.80061 1. 0. 0.
297	1
298	-0.586638 -1.38326 -2.92321 0.438062 -2.68776 -2.23921 1.75376 -0.319055 -2.99941 1. 0. 0.
299	1
300	-1.64154 -3.70136 -1.80061 -2.50954 -2.13946 -1.80561 -4.18614 -2.49696 -0.640907 1. 0. 0.
301	1
302	-1.64154 -3.70136 -1.80061 -4.18614 -2.49696 -0.640907 -3.92214 -3.45776 0.834093 1. 0. 0.
303	1
304	-1.53704 -3.60006 0.497793 -1.64154 -3.70136 -1.80061 -3.92214 -3.45776 0.834093 1. 0. 0.
305	1
306	0.904762 -3.62316 -0.490507 -1.53704 -3.60006 0.497793 -1.64154 -3.70136 -1.80061 1. 0. 0.
307	1
308	0.777562 -3.65286 1.28459 0.904762 -3.62316 -0.490507 -1.53704 -3.60006 0.497793 1. 0. 0.
309	1
310	0.904762 -3.62316 -0.490507 0.438062 -2.68776 -2.23921 -1.64154 -3.70136 -1.80061 1. 0. 0.
311	1
312	-4.76454 -1.89276 0.930293 -4.18614 -2.49696 -0.640907 -3.92214 -3.45776 0.834093 1. 0. 0.
313	1
314	-4.76454 -1.89276 0.930293 -4.18614 -2.49696 -0.640907 -6.29174 0.967445 0.583993 1. 0. 0.
315	1
316	-4.18614 -2.49696 -0.640907 -6.29174 0.967445 0.583993 -6.43904 1.78854 -0.988307 1. 0. 0.
317	1
318	-6.29174 0.967445 0.583993 -7.12784 2.53484 0.473393 -6.43904 1.78854 -0.988307 1. 0. 0.
319	1
320	3.60736 1.29684 -2.87381 5.67566 1.42984 -1.78291 5.10266 2.74254 -0.715907 1. 0. 0.
321	1
322	5.67566 1.42984 -1.78291 5.10266 2.74254 -0.715907 7.55546 2.01984 -0.0120068 1. 0. 0.
323	1
324	-5.13424 3.87154 -1.43691 -7.12784 2.53484 0.473393 -6.43904 1.78854 -0.988307 1. 0. 0.
325	1
326	-5.82304 4.61784 0.0247932 -5.13424 3.87154 -1.43691 -7.12784 2.53484 0.473393 1. 0. 0.
327	1
328	-5.82304 4.61784 0.0247932 -4.05744 4.53424 -0.184207 -5.13424 3.87154 -1.43691 1. 0. 0.
329	9
330	# terminating special property
331	# current virtual sphere
332	8
333	25.0 0.6 -1.0 -1.0 -1.0 0.2 0 0 0 0
334	2
335	-5.0049 4.34121 -0.532107 5 1 0 0
336	9
337	terminating special property

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