FixInternals test numerically unstable [was: ase test failed]
ase test has 1 failed
I want to install ASE in my WSL2, the system is Ubuntu-20.04.
Because I am using Anaconda, so I did all the following in my new environment which have NumPy, Scipy and Matplotlib packages installed through conda install command.
I installed ase through pip command $ pip install --upgrade --user ase and added the ase binaries to the environment variable $PATH.
I have tried to run the ase test command another time, but same error still presented.
Please let me know if there are extra messages you need to know and help me with this issue!
One failure showed up after I ran ase test in command line. Here is the output:
[gw22] [ 99%] FAILED constraints/test_fixinternals.py::test_combos
constraints/test_fixinternals.py::test_index_shuffle
[gw22] [ 99%] PASSED constraints/test_fixinternals.py::test_index_shuffle
constraints/test_fixinternals.py::test_combo_index_shuffle
[gw22] [ 99%] PASSED constraints/test_fixinternals.py::test_combo_index_shuffle
[gw3] [ 99%] PASSED forcefields/test_combine_mm2.py::test_combine_mm2
forcefields/test_counterions.py::test_counterions
[gw3] [ 99%] PASSED forcefields/test_counterions.py::test_counterions
forcefields/test_forceqmmm.py::test_forceqmmm
[gw0] [ 99%] PASSED ga/test_bulk_operators.py::test_bulk_operators[0]
[gw3] [ 99%] PASSED forcefields/test_forceqmmm.py::test_forceqmmm
forcefields/test_qmmm.py::test_qmmm
[gw3] [ 99%] PASSED forcefields/test_qmmm.py::test_qmmm
[gw14] [ 99%] PASSED neb/test_dynamic_neb.py::test_dynamic_neb
neb/test_idpp.py::test_idpp
[gw14] [ 99%] PASSED neb/test_idpp.py::test_idpp
[gw4] [ 99%] PASSED precon/test_ff_and_precon_c60.py::test_opt_no_precon
precon/test_ff_and_precon_c60.py::test_opt_with_precon
[gw4] [100%] SKIPPED precon/test_ff_and_precon_c60.py::test_opt_with_precon
======================================================= FAILURES =======================================================
_____________________________________________________ test_combos ______________________________________________________
[gw22] linux -- Python 3.9.2 /home/youmu/anaconda3/envs/jkitchin_dft/bin/python
def test_combos():
(atoms, constr, bondcombo_def, target_bondcombo, anglecombo_def,
target_anglecombo, dihedralcombo_def,
target_dihedralcombo) = setup_combos()
ref_bondcombo = get_bondcombo(atoms, bondcombo_def)
ref_anglecombo = get_anglecombo(atoms, anglecombo_def)
ref_dihedralcombo = get_dihedralcombo(atoms, dihedralcombo_def)
atoms.calc = EMT()
atoms.set_constraint(constr)
opt = BFGS(atoms)
> opt.run(fmax=0.01)
/home/youmu/.local/lib/python3.9/site-packages/ase/test/constraints/test_fixinternals.py:144:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/home/youmu/.local/lib/python3.9/site-packages/ase/optimize/optimize.py:294: in run
return Dynamics.run(self)
/home/youmu/.local/lib/python3.9/site-packages/ase/optimize/optimize.py:181: in run
for converged in Dynamics.irun(self):
/home/youmu/.local/lib/python3.9/site-packages/ase/optimize/optimize.py:160: in irun
self.step()
/home/youmu/.local/lib/python3.9/site-packages/ase/optimize/bfgs.py:107: in step
atoms.set_positions(r + dr)
/home/youmu/.local/lib/python3.9/site-packages/ase/atoms.py:693: in set_positions
constraint.adjust_positions(self, newpositions)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = FixInternals(_copy_init=[FixBondCombo(0.1779485447661857, [[2, 1], [2, 3]], [ 1. -1.]), FixAngleCombo(201.467424611547... 8], [7, 0, 6]], [1. 1.]), FixDihedralCombo(396.39755637384025, [[3, 2, 1, 4], [2, 1, 0, 7]], [1. 1.])], epsilon=1e-10)
atoms = Atoms(symbols='C2OH6', pbc=False, cell=[14.062514, 12.244742, 11.773866], constraint=FixInternals(_copy_init=[FixBondC....]), FixDihedralCombo(396.39755637384025, [[3, 2, 1, 4], [2, 1, 0, 7]], [1. 1.])], epsilon=1e-10), calculator=EMT(...))
new = array([[ 8.09754998e+00, 5.28149856e+00, 5.79763001e+00],
[ 1.67555133e+10, 7.91312268e+09, -6.31574247e+09]... [ 6.73059947e+00, 7.19470020e+00, 8.06127934e+00],
[ 7.25942740e+00, 6.00301330e+00, 3.91769514e+00]])
def adjust_positions(self, atoms, new):
self.initialize(atoms)
for constraint in self.constraints:
constraint.prepare_jacobian(atoms.positions)
for j in range(50):
maxerr = 0.0
for constraint in self.constraints:
constraint.adjust_positions(atoms.positions, new)
maxerr = max(abs(constraint.sigma), maxerr)
if maxerr < self.epsilon:
return
> raise ValueError('Shake did not converge.')
E ValueError: Shake did not converge.
/home/youmu/.local/lib/python3.9/site-packages/ase/constraints.py:917: ValueError
------------------------------------------------- Captured stdout call -------------------------------------------------
Step Time Energy fmax
BFGS: 0 13:29:54 39.657895 73.8923
BFGS: 1 13:29:54 10.644302 22.4925
BFGS: 2 13:29:54 5.443498 12.6165
BFGS: 3 13:29:54 2.515231 6.0965
BFGS: 4 13:29:54 1.940941 2.0156
BFGS: 5 13:29:54 1.788119 1.0186
BFGS: 6 13:29:54 1.748545 0.3646
BFGS: 7 13:29:54 1.743149 0.1977
BFGS: 8 13:29:54 1.740182 0.2001
BFGS: 9 13:29:54 1.737209 0.2001
BFGS: 10 13:29:54 1.732274 0.2528
BFGS: 11 13:29:54 1.720366 0.3780
BFGS: 12 13:29:54 1.663077 1.1331
BFGS: 13 13:29:54 1.709219 2.1993
BFGS: 14 13:29:54 1.632439 1.2758
BFGS: 15 13:29:54 1.610038 1.2494
BFGS: 16 13:29:54 1.538051 1.1844
BFGS: 17 13:29:54 1.458670 0.6763
BFGS: 18 13:29:54 1.429438 0.4229
BFGS: 19 13:29:54 1.416391 0.2376
BFGS: 20 13:29:54 1.413481 0.1524
BFGS: 21 13:29:54 1.410853 0.1548
BFGS: 22 13:29:54 1.409166 0.1443
BFGS: 23 13:29:54 1.406738 0.1995
BFGS: 24 13:29:54 1.404419 0.2606
BFGS: 25 13:29:54 1.400377 0.2945
BFGS: 26 13:29:54 1.394286 0.2409
BFGS: 27 13:29:54 1.389319 0.2656
BFGS: 28 13:29:54 1.385119 0.1634
BFGS: 29 13:29:54 1.383420 0.1035
BFGS: 30 13:29:54 1.382569 0.0905
BFGS: 31 13:29:54 1.381133 0.1309
BFGS: 32 13:29:54 1.378734 0.1954
BFGS: 33 13:29:54 1.373767 0.2600
BFGS: 34 13:29:54 1.367556 0.3735
BFGS: 35 13:29:55 1.362541 0.3594
BFGS: 36 13:29:55 1.356740 0.2363
BFGS: 37 13:29:55 1.350912 0.2316
BFGS: 38 13:29:55 1.345278 0.2040
BFGS: 39 13:29:55 1.338644 0.1972
BFGS: 40 13:29:55 1.331724 0.1291
BFGS: 41 13:29:55 1.330038 0.1061
BFGS: 42 13:29:55 1.330165 0.1167
BFGS: 43 13:29:55 1.329083 0.0767
BFGS: 44 13:29:55 1.328689 0.0914
BFGS: 45 13:29:55 1.327897 0.1280
BFGS: 46 13:29:55 1.326861 0.1426
BFGS: 47 13:29:55 1.325539 0.1324
BFGS: 48 13:29:55 1.324139 0.1733
BFGS: 49 13:29:55 1.322799 0.1665
BFGS: 50 13:29:55 1.321678 0.1109
BFGS: 51 13:29:55 1.320888 0.0770
BFGS: 52 13:29:55 1.320523 0.0602
BFGS: 53 13:29:55 1.320409 0.0842
BFGS: 54 13:29:55 1.320321 0.1007
BFGS: 55 13:29:55 1.320049 0.1276
BFGS: 56 13:29:55 1.319370 0.1609
BFGS: 57 13:29:55 1.317862 0.1877
BFGS: 58 13:29:55 1.315649 0.1684
BFGS: 59 13:29:55 1.314385 0.1398
BFGS: 60 13:29:55 1.313562 0.0996
BFGS: 61 13:29:55 1.312850 0.0900
BFGS: 62 13:29:55 1.312399 0.0430
BFGS: 63 13:29:55 1.312372 0.0419
BFGS: 64 13:29:55 1.312318 0.0410
BFGS: 65 13:29:55 1.312201 0.0556
BFGS: 66 13:29:55 1.312104 0.0634
BFGS: 67 13:29:55 1.311870 0.0805
BFGS: 68 13:29:55 1.311669 0.0844
BFGS: 69 13:29:55 1.311352 0.0761
BFGS: 70 13:29:55 1.311084 0.0623
BFGS: 71 13:29:55 1.310783 0.0449
BFGS: 72 13:29:55 1.310604 0.0447
BFGS: 73 13:29:55 1.310416 0.0527
BFGS: 74 13:29:55 1.310101 0.0621
BFGS: 75 13:29:55 1.309978 0.0653
BFGS: 76 13:29:55 1.309937 0.0791
BFGS: 77 13:29:55 1.309939 0.0992
BFGS: 78 13:29:55 1.309955 0.1089
BFGS: 79 13:29:55 1.310033 0.1208
BFGS: 80 13:29:56 1.310050 0.1217
BFGS: 81 13:29:56 1.309992 0.1219
BFGS: 82 13:29:56 1.309959 0.1217
BFGS: 83 13:29:56 1.309862 0.1285
BFGS: 84 13:29:56 1.309411 0.1587
BFGS: 85 13:29:56 1.311224 0.2942
BFGS: 86 13:29:56 1.307258 0.1505
BFGS: 87 13:29:56 1.305675 0.1329
BFGS: 88 13:29:56 1.311650 0.3582
BFGS: 89 13:29:56 1.305986 0.1779
BFGS: 90 13:29:56 1.303022 0.1346
BFGS: 91 13:29:56 1.303258 0.1702
BFGS: 92 13:29:56 1.302181 0.1119
BFGS: 93 13:29:56 1.301732 0.1131
BFGS: 94 13:29:56 1.300449 0.1634
BFGS: 95 13:29:56 1.299966 0.1379
BFGS: 96 13:29:56 1.299409 0.1133
BFGS: 97 13:29:56 1.298911 0.0875
BFGS: 98 13:29:56 1.298179 0.0912
BFGS: 99 13:29:56 1.296035 0.0952
BFGS: 100 13:29:56 1.294730 0.0806
BFGS: 101 13:29:56 1.292732 0.0725
BFGS: 102 13:29:56 1.292265 0.0764
BFGS: 103 13:29:56 1.291546 0.0529
BFGS: 104 13:29:56 1.291317 0.0889
BFGS: 105 13:29:56 1.291038 0.0493
BFGS: 106 13:29:56 1.290860 0.0424
BFGS: 107 13:29:56 1.290584 0.0217
BFGS: 108 13:29:56 1.290457 0.0157
BFGS: 109 13:29:56 1.290429 0.0256
BFGS: 110 13:29:56 1.290416 0.0239
BFGS: 111 13:29:56 1.290399 0.0268
BFGS: 112 13:29:56 1.290386 0.0265
BFGS: 113 13:29:56 1.290343 0.0249
BFGS: 114 13:29:56 1.290268 0.0429
BFGS: 115 13:29:56 1.289985 0.1010
BFGS: 116 13:29:56 1.291131 0.2930
BFGS: 117 13:29:56 1.289464 0.1204
BFGS: 118 13:29:56 1.288972 0.1235
BFGS: 119 13:29:56 1.296570 0.3559
BFGS: 120 13:29:56 1.346520 0.8007
BFGS: 121 13:29:56 1.288318 0.1047
BFGS: 122 13:29:56 1.284925 0.0819
BFGS: 123 13:29:56 1.284367 0.0639
BFGS: 124 13:29:56 1.284153 0.0568
BFGS: 125 13:29:56 1.283888 0.0217
BFGS: 126 13:29:56 1.284012 0.0591
BFGS: 127 13:29:56 1.283740 0.0373
BFGS: 128 13:29:56 1.283555 0.0524
BFGS: 129 13:29:56 1.283417 0.1019
BFGS: 130 13:29:56 1.283172 0.0673
BFGS: 131 13:29:56 1.282902 0.0385
BFGS: 132 13:29:56 1.282816 0.0245
BFGS: 133 13:29:56 1.282825 0.0396
BFGS: 134 13:29:56 1.282820 0.0404
BFGS: 135 13:29:56 1.282734 0.0437
BFGS: 136 13:29:56 1.282693 0.0440
BFGS: 137 13:29:56 1.282651 0.0545
BFGS: 138 13:29:57 1.282620 0.0579
BFGS: 139 13:29:57 1.282621 0.0660
BFGS: 140 13:29:57 1.282612 0.0652
BFGS: 141 13:29:57 1.282587 0.0622
BFGS: 142 13:29:57 1.282510 0.0490
BFGS: 143 13:29:57 1.282381 0.0282
BFGS: 144 13:29:57 1.282258 0.0214
BFGS: 145 13:29:57 1.282172 0.0221
BFGS: 146 13:29:57 1.281923 0.0612
from ase import Atoms
BFGS: 147 13:29:57 1.282085 0.1067
BFGS: 148 13:29:57 1.282042 0.0964
BFGS: 149 13:29:57 1.282127 0.1054
BFGS: 150 13:29:57 1.281659 0.0754
BFGS: 151 13:29:57 1.281643 0.1249
BFGS: 152 13:29:57 1.284892 0.2924
BFGS: 153 13:29:57 1.284612 0.2449
BFGS: 154 13:29:57 1.282654 0.2340
BFGS: 155 13:29:57 1.288413 0.4097
BFGS: 156 13:29:57 1.287209 0.3743
BFGS: 157 13:29:57 1.290762 0.5096
BFGS: 158 13:29:57 1.291332 0.5189
BFGS: 159 13:29:57 1.290773 0.5134
BFGS: 160 13:29:57 1.290893 0.5092
BFGS: 161 13:29:57 1.297931 0.6724
----------------------------------------------- Captured stdout teardown -----------------------------------------------
Testpath: /tmp/pytest-of-youmu/pytest-1/popen-gw22/test_combos0
. /usr/share/bash-completion/bash_completion
=============================================== short test summary info ================================================
FAILED constraints/test_fixinternals.py::test_combos - ValueError: Shake did not converge.
=============================== 1 failed, 1483 passed, 265 skipped, 3 xfailed in 48.73s ================================Edited by Ask Hjorth Larsen