source: tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data@ 77d0cd

AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
Last change on this file since 77d0cd was 075357, checked in by Frederik Heber <frederik.heber@…>, 8 years ago

TEST: Adding Python test on ForceAnnealing using an Ising model with and without bondgraph.

  • We are not done yet with implementing optimization using the bond graph. The 2-body Ising test on using bond graph reveals that we have a problem when bonds need to shrink. In case of the test the updates from either side cancel each other and there is no progress. For the 5-body Ising test convergence is not monotone, probably also because of the need to proper deal with shrinking bonds.
  • TESTS: As Python ForceAnnealing test use numpy to compute damping_factor we have added a check for numpy presence and skip tests otherwise.
  • TESTFIX: Marked Python tests on ForceAnnealing using the bond graph as XFAIL because of this.
  • Property mode set to 100644
File size: 5.8 KB
RevLine 
[075357]1# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
2# Box 20 0 0 0 20 0 0 0 20
3C 1 6 10 10 0 0 0 0 0 0 2 0 0 0
4C 2 7.6 10 10 0 0 0 0 0 0 1 3 0 0
5C 3 8.7 10 10 0 0 0 0 0 0 2 4 0 0
6C 4 10.8 10 10 0 0 0 0 0 0 3 5 0 0
7C 5 12.4 10 10 0 0 0 0 0 0 4 0 0 0
8# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
9C 1 6 10 10 0 0 0 0 0 0 2 0 0 0
10C 2 7.57354 10 10 0 0 0 -0.264589 0 0 1 3 0 0
11C 3 8.75292 10 10 0 0 0 0.529177 0 0 2 4 0 0
12C 4 10.7735 10 10 0 0 0 -0.264589 0 0 3 5 0 0
13C 5 12.4 10 10 0 0 0 0 0 0 4 0 0 0
14# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
15C 1 5.99762 10 10 0 0 0 -0.014002 0 0 2 0 0 0
16C 2 7.55664 10 10 0 0 0 -0.208581 0 0 1 3 0 0
17C 3 8.79358 10 10 0 0 0 0.445144 0 0 2 4 0 0
18C 4 10.7566 10 10 0 0 0 -0.208538 0 0 3 5 0 0
19C 5 12.3976 10 10 0 0 0 -0.0140232 0 0 4 0 0 0
20# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
21C 1 6.00099 10 10 0 0 0 -0.0216857 0 0 2 0 0 0
22C 2 7.54962 10 10 0 0 0 -0.170437 0 0 1 3 0 0
23C 3 8.88895 10 10 0 0 0 0.384225 0 0 2 4 0 0
24C 4 10.7496 10 10 0 0 0 -0.170406 0 0 3 5 0 0
25C 5 12.401 10 10 0 0 0 -0.0216963 0 0 4 0 0 0
26# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
27C 1 6.01638 10 10 0 0 0 -0.0271838 0 0 2 0 0 0
28C 2 7.58211 10 10 0 0 0 -0.110757 0 0 1 3 0 0
29C 3 9.04595 10 10 0 0 0 0.275871 0 0 2 4 0 0
30C 4 10.7821 10 10 0 0 0 -0.11073 0 0 3 5 0 0
31C 5 12.4164 10 10 0 0 0 -0.0271997 0 0 4 0 0 0
32# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
33C 1 5.98362 10 10 0 0 0 -0.0181349 0 0 2 0 0 0
34C 2 7.58977 10 10 0 0 0 -0.0539179 0 0 1 3 0 0
35C 3 9.13561 10 10 0 0 0 0.1441 0 0 2 4 0 0
36C 4 10.7898 10 10 0 0 0 -0.0538967 0 0 3 5 0 0
37C 5 12.3835 10 10 0 0 0 -0.0181508 0 0 4 0 0 0
38# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
39C 1 5.98766 10 10 0 0 0 0.00325444 0 0 2 0 0 0
40C 2 7.59245 10 10 0 0 0 -0.0319147 0 0 1 3 0 0
41C 3 9.15835 10 10 0 0 0 0.0573364 0 0 2 4 0 0
42C 4 10.7925 10 10 0 0 0 -0.0320099 0 0 3 5 0 0
43C 5 12.3876 10 10 0 0 0 0.00333382 0 0 4 0 0 0
44# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
45C 1 5.98842 10 10 0 0 0 0.00253476 0 0 2 0 0 0
46C 2 7.59255 10 10 0 0 0 -0.0205797 0 0 1 3 0 0
47C 3 9.16535 10 10 0 0 0 0.0361163 0 0 2 4 0 0
48C 4 10.7926 10 10 0 0 0 -0.0206644 0 0 3 5 0 0
49C 5 12.3884 10 10 0 0 0 0.00259297 0 0 4 0 0 0
50# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
51C 1 5.99017 10 10 0 0 0 0.0021855 0 0 2 0 0 0
52C 2 7.59433 10 10 0 0 0 -0.0165791 0 0 1 3 0 0
53C 3 9.17263 10 10 0 0 0 0.0288137 0 0 2 4 0 0
54C 4 10.7943 10 10 0 0 0 -0.0166426 0 0 3 5 0 0
55C 5 12.3901 10 10 0 0 0 0.00222254 0 0 4 0 0 0
56# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
57C 1 5.99673 10 10 0 0 0 0.00220138 0 0 2 0 0 0
58C 2 7.59359 10 10 0 0 0 -0.0136845 0 0 1 3 0 0
59C 3 9.1839 10 10 0 0 0 0.0229504 0 0 2 4 0 0
60C 4 10.7936 10 10 0 0 0 -0.0136898 0 0 3 5 0 0
61C 5 12.3961 10 10 0 0 0 0.00222254 0 0 4 0 0 0
62# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
63C 1 5.99607 10 10 0 0 0 -0.00166162 0 0 2 0 0 0
64C 2 7.59504 10 10 0 0 0 -0.00346611 0 0 1 3 0 0
65C 3 9.19027 10 10 0 0 0 0.0102607 0 0 2 4 0 0
66C 4 10.7951 10 10 0 0 0 -0.00381008 0 0 3 5 0 0
67C 5 12.3957 10 10 0 0 0 -0.00132294 0 0 4 0 0 0
68# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
69C 1 5.99616 10 10 0 0 0 -0.000545053 0 0 2 0 0 0
70C 2 7.59523 10 10 0 0 0 -0.00197912 0 0 1 3 0 0
71C 3 9.192 10 10 0 0 0 0.0050801 0 0 2 4 0 0
72C 4 10.7952 10 10 0 0 0 -0.00223842 0 0 3 5 0 0
73C 5 12.3959 10 10 0 0 0 -0.000317506 0 0 4 0 0 0
74# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
75C 1 5.99623 10 10 0 0 0 -0.000492135 0 0 2 0 0 0
76C 2 7.59535 10 10 0 0 0 -0.00121711 0 0 1 3 0 0
77C 3 9.19284 10 10 0 0 0 0.00340261 0 0 2 4 0 0
78C 4 10.7954 10 10 0 0 0 -0.00132294 0 0 3 5 0 0
79C 5 12.3959 10 10 0 0 0 -0.000370424 0 0 4 0 0 0
80# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
81C 1 5.99613 10 10 0 0 0 -0.000465676 0 0 2 0 0 0
82C 2 7.59549 10 10 0 0 0 -0.000862559 0 0 1 3 0 0
83C 3 9.19376 10 10 0 0 0 0.00268293 0 0 2 4 0 0
84C 4 10.7955 10 10 0 0 0 -0.00109011 0 0 3 5 0 0
85C 5 12.3959 10 10 0 0 0 -0.000264589 0 0 4 0 0 0
86# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
87C 1 5.99613 10 10 0 0 0 -0.000338673 0 0 2 0 0 0
88C 2 7.59563 10 10 0 0 0 -0.000576803 0 0 1 3 0 0
89C 3 9.19481 10 10 0 0 0 0.00183625 0 0 2 4 0 0
90C 4 10.7956 10 10 0 0 0 -0.000709098 0 0 3 5 0 0
91C 5 12.3959 10 10 0 0 0 -0.000211671 0 0 4 0 0 0
92# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
93C 1 5.99618 10 10 0 0 0 -0.000264589 0 0 2 0 0 0
94C 2 7.59572 10 10 0 0 0 -0.000169337 0 0 1 3 0 0
95C 3 9.1953 10 10 0 0 0 0.000851975 0 0 2 4 0 0
96C 4 10.7957 10 10 0 0 0 -0.000259297 0 0 3 5 0 0
97C 5 12.3959 10 10 0 0 0 -0.000158753 0 0 4 0 0 0
98# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
99C 1 5.99613 10 10 0 0 0 -0.000243422 0 0 2 0 0 0
100C 2 7.59576 10 10 0 0 0 2.11671e-05 0 0 1 3 0 0
101C 3 9.19545 10 10 0 0 0 0.000433925 0 0 2 4 0 0
102C 4 10.7957 10 10 0 0 0 -0.000105835 0 0 3 5 0 0
103C 5 12.396 10 10 0 0 0 -0.000105835 0 0 4 0 0 0
104# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
105C 1 5.99607 10 10 0 0 0 -0.000195796 0 0 2 0 0 0
106C 2 7.59579 10 10 0 0 0 3.17506e-05 0 0 1 3 0 0
107C 3 9.19554 10 10 0 0 0 0.000296339 0 0 2 4 0 0
108C 4 10.7957 10 10 0 0 0 2.64589e-05 0 0 3 5 0 0
109C 5 12.396 10 10 0 0 0 -0.000158753 0 0 4 0 0 0
110# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
111C 1 5.99606 10 10 0 0 0 -0.00014817 0 0 2 0 0 0
112C 2 7.59591 10 10 0 0 0 1.58753e-05 0 0 1 3 0 0
113C 3 9.19566 10 10 0 0 0 0.000216963 0 0 2 4 0 0
114C 4 10.7958 10 10 0 0 0 7.40848e-05 0 0 3 5 0 0
115C 5 12.396 10 10 0 0 0 -0.000158753 0 0 4 0 0 0
116# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
117C 1 5.99609 10 10 0 0 0 -7.93766e-05 0 0 2 0 0 0
118C 2 7.59594 10 10 0 0 0 -5.29177e-05 0 0 1 3 0 0
119C 3 9.19599 10 10 0 0 0 0.000206379 0 0 2 4 0 0
120C 4 10.7961 10 10 0 0 0 3.17506e-05 0 0 3 5 0 0
121C 5 12.3961 10 10 0 0 0 -0.000105835 0 0 4 0 0 0
122# ATOMDATA type Id x=3 u=3 F=3 neighbors=4
123C 1 5.99608 10 10 0 0 0 -7.93766e-05 0 0 2 0 0 0
124C 2 7.59598 10 10 0 0 0 0.000105835 0 0 1 3 0 0
125C 3 9.19602 10 10 0 0 0 3.17506e-05 0 0 2 4 0 0
126C 4 10.796 10 10 0 0 0 -5.82095e-05 0 0 3 5 0 0
127C 5 12.396 10 10 0 0 0 -2.71051e-21 0 0 4 0 0 0
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