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Published
20 hours ago •
dftbplus
dftbplus
About the stability of GFN2-xTB in MD
Describe the bug Many thanks for implementing the xTB Hamiltonian in dftb+ @awvwgk So I would like to rerun the recipes/moleculardynamics/md/dftb_in.hsd with GFN2-xTB Hamiltonian. from https://dftbplus-recipes.readthedocs.io/en/latest/introduction.html and file https://dftbplus-recipes.readthedocs.io/en/latest/_downloads/d18327310bfd7b419944887ab36a50fa/recipes.tar.bz2
To Reproduce I replace the section of
Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1E-6
Filling = Fermi {
Temperature [Kelvin] = 400
}
SlaterKosterFiles = Type2FileNames {
Prefix = "../../slakos/mio-ext/"
Separator = "-"
Suffix = ".skf"
}
MaxAngularMomentum = {
H = "s"
O = "p"
C = "p"
}
}
With
Hamiltonian = xTB {
Method = "GFN2-xTB"
}
And I got scf non-convergence in step 2 after 100 steps of SCF iterations. The DFTB+ is conda version 21.2
The full output
|===============================================================================
|
| DFTB+ release 21.2
|
| Copyright (C) 2006 - 2021 DFTB+ developers group
|
|===============================================================================
|
| When publishing results obtained with DFTB+, please cite the following
| reference:
|
| * DFTB+, a software package for efficient approximate density functional
| theory based atomistic simulations, J. Chem. Phys. 152, 124101 (2020).
| [doi: 10.1063/1.5143190]
|
| You should also cite additional publications crediting the parametrization
| data you use. Please consult the documentation of the SK-files for the
| references.
|
|===============================================================================
Reading input file 'dftb_in.hsd'
Parser version: 10
--------------------------------------------------------------------------------
*** Converting input from parser version 7 to parser version 10 ...
*** Done.
WARNING!
-> Settings will be read but ignored (compiled without MPI support)
Path: dftbplusinput/Parallel
Line: 122-124 (File: dftb_in.hsd)
Processed input in HSD format written to 'dftb_pin.hsd'
Starting initialization...
--------------------------------------------------------------------------------
OpenMP threads: 10
Specified random seed: 3871906
Mode: MD without scaling of velocities
(a.k.a. NVE ensemble)
Self consistent charges: Yes
SCC-tolerance: 0.100000E-04
Max. scc iterations: 100
Shell resolved Hubbard: Yes
Spin polarisation: No
Nr. of up electrons: 70.000000
Nr. of down electrons: 70.000000
Periodic boundaries: No
Electronic solver: Relatively robust
Mixer: Broyden mixer
Mixing parameter: 0.200000
Maximal SCC-cycles: 100
Nr. of chrg. vec. in memory: 100
tblite library version: 0.1.0
-> parametrization: GFN2-xTB
-> repulsion: Yes
-> dispersion: Yes
-> halogen bonding: No
-> electrostatics: Yes
-> isotropic: Yes
-> anisotropic: Yes
-> third-order: Yes
Electronic temperature: 0.950045E-03 H 0.258520E-01 eV
Time step: 0.206707E+02
Initial charges: Set automatically (system chrg: 0.000E+00)
Included shells: C: s, p
O: s, p
H: s
Extra options:
Mulliken analysis
Force type original
--------------------------------------------------------------------------------
*** Geometry step: 0
iSCC Total electronic Diff electronic SCC error
1 0.00000000E+00 0.00000000E+00 0.11696846E+01
2 -0.79107708E+02 -0.79107708E+02 0.67793583E+00
3 -0.79771264E+02 -0.66355546E+00 0.19474322E+00
4 -0.79903958E+02 -0.13269382E+00 0.19561020E+00
5 -0.79922857E+02 -0.18899358E-01 0.61264317E-01
6 -0.79937486E+02 -0.14628740E-01 0.33366140E-01
7 -0.79939491E+02 -0.20046472E-02 0.68206438E-02
8 -0.79940244E+02 -0.75307232E-03 0.40804269E-02
9 -0.79940285E+02 -0.41417558E-04 0.15394052E-02
10 -0.79940291E+02 -0.56960161E-05 0.80512866E-03
11 -0.79940291E+02 -0.41854764E-06 0.10710892E-02
12 -0.79940291E+02 0.25183979E-06 0.99104710E-04
13 -0.79940291E+02 -0.52767579E-06 0.68904223E-04
14 -0.79940291E+02 -0.38515964E-08 0.84650537E-04
15 -0.79940291E+02 0.29550051E-08 0.11216059E-04
16 -0.79940291E+02 -0.40035530E-08 0.49967814E-05
Total Energy: -79.9402914091 H -2175.2860 eV
Extrapolated to 0K: -79.9402914091 H -2175.2860 eV
Total Mermin free energy: -79.9402914091 H -2175.2860 eV
Force related energy: -79.9402914091 H -2175.2860 eV
>> Charges saved for restart in charges.bin
MD Temperature: 0.0000007439 H 0.2349 K
MD Kinetic Energy: 0.0000412863 H 0.0011 eV
Total MD Energy: -79.9402501228 H -2175.2849 eV
--------------------------------------------------------------------------------
*** Geometry step: 1
iSCC Total electronic Diff electronic SCC error
1 -0.79940291E+02 0.00000000E+00 0.10962147E+01
2 -0.74513050E+02 0.54272411E+01 0.11872032E+01
3 -0.74495854E+02 0.17196342E-01 0.11078267E+01
4 -0.74700912E+02 -0.20505809E+00 0.11390840E+01
5 -0.75179321E+02 -0.47840867E+00 0.10980534E+01
6 -0.74489410E+02 0.68991111E+00 0.44207321E+00
7 -0.75557535E+02 -0.10681250E+01 0.34545891E+00
8 -0.75648783E+02 -0.91248213E-01 0.45540706E+00
9 -0.75541736E+02 0.10704728E+00 0.67813058E+00
10 -0.75597643E+02 -0.55907602E-01 0.23266552E+00
11 -0.75656425E+02 -0.58781845E-01 0.11521174E+00
12 -0.75672058E+02 -0.15632631E-01 0.57099416E-01
13 -0.75676917E+02 -0.48597206E-02 0.65010494E-01
14 -0.75677907E+02 -0.98986287E-03 0.39548719E-01
15 -0.75678492E+02 -0.58436270E-03 0.28972863E-01
16 -0.75678648E+02 -0.15660133E-03 0.66764066E-02
17 -0.75678759E+02 -0.11065216E-03 0.11300546E-01
18 -0.75678757E+02 0.21479023E-05 0.51655614E-02
19 -0.75678786E+02 -0.29136709E-04 0.18118920E-02
20 -0.75678795E+02 -0.87855742E-05 0.23845121E-02
21 -0.75678796E+02 -0.16838372E-05 0.33664604E-03
22 -0.75678797E+02 -0.98411273E-06 0.28273899E-03
23 -0.75678796E+02 0.13555434E-05 0.35798191E-04
24 -0.75678797E+02 -0.79312944E-06 0.36480260E-03
25 -0.75678797E+02 0.79403577E-08 0.46972962E-04
26 -0.75678797E+02 -0.22149720E-07 0.81158298E-04
27 -0.75678797E+02 0.60987020E-08 0.23790493E-04
28 -0.75678797E+02 -0.41902581E-07 0.10950397E-04
29 -0.75678797E+02 0.39800767E-08 0.14573480E-05
Total Energy: -75.6787968201 H -2059.3248 eV
Extrapolated to 0K: -75.6796566273 H -2059.3482 eV
Total Mermin free energy: -75.6805164346 H -2059.3716 eV
Force related energy: -75.6805164346 H -2059.3716 eV
>> Charges saved for restart in charges.bin
MD Temperature: 17.9040170191 H 5653634.6667 K
MD Kinetic Energy: 993.6729445577 H 27039.2166 eV
Total MD Energy: 917.9924281232 H 24979.8449 eV
--------------------------------------------------------------------------------
*** Geometry step: 2
iSCC Total electronic Diff electronic SCC error
1 -0.75678797E+02 0.00000000E+00 0.43343091E+01
2 -0.31721606E+02 0.43957191E+02 0.49301603E+01
3 0.10597109E+02 0.42318715E+02 0.37461155E+01
4 -0.38458258E+02 -0.49055367E+02 0.29503637E+01
5 -0.49389625E+02 -0.10931367E+02 0.28758136E+01
6 -0.48758180E+02 0.63144507E+00 0.33523940E+01
7 -0.46358937E+02 0.23992427E+01 0.31203962E+01
8 -0.46669050E+02 -0.31011272E+00 0.28893868E+01
9 -0.48776810E+02 -0.21077600E+01 0.28843846E+01
10 -0.51708038E+02 -0.29312285E+01 0.28846697E+01
11 -0.51960403E+02 -0.25236511E+00 0.29211539E+01
12 -0.51186911E+02 0.77349230E+00 0.29142271E+01
13 -0.50861433E+02 0.32547831E+00 0.45778767E+01
14 -0.33930689E+02 0.16930744E+02 0.45478757E+01
15 -0.37987296E+02 -0.40566073E+01 0.35104192E+01
16 -0.45741357E+02 -0.77540608E+01 0.46172631E+01
17 -0.42817021E+02 0.29243359E+01 0.34698370E+01
18 -0.48677348E+02 -0.58603270E+01 0.45481854E+01
19 -0.38165294E+02 0.10512054E+02 0.45093199E+01
20 -0.22593214E+02 0.15572080E+02 0.44215013E+01
21 -0.36980547E+02 -0.14387333E+02 0.38098051E+01
22 -0.37857867E+02 -0.87731990E+00 0.44177909E+01
23 -0.36561720E+02 0.12961466E+01 0.43587805E+01
24 -0.16162184E+02 0.20399536E+02 0.41920371E+01
25 -0.35149136E+02 -0.18986952E+02 0.43434170E+01
26 -0.30272387E+02 0.48767493E+01 0.42120503E+01
27 -0.28546389E+02 0.17259977E+01 0.43990927E+01
28 -0.33403070E+02 -0.48566806E+01 0.43505830E+01
29 -0.26561417E+02 0.68416526E+01 0.43474828E+01
30 -0.28248858E+02 -0.16874406E+01 0.43552719E+01
31 -0.32198959E+02 -0.39501017E+01 0.43676558E+01
32 -0.37376327E+02 -0.51773677E+01 0.44170215E+01
33 -0.28853878E+02 0.85224495E+01 0.44546410E+01
34 -0.28753160E+02 0.10071762E+00 0.44383267E+01
35 -0.29168131E+02 -0.41497085E+00 0.44257775E+01
36 -0.27379148E+02 0.17889827E+01 0.43993081E+01
37 -0.35457878E+02 -0.80787295E+01 0.44025839E+01
38 -0.33060990E+02 0.23968883E+01 0.44070721E+01
39 -0.35071346E+02 -0.20103566E+01 0.44063700E+01
40 -0.33127046E+02 0.19442998E+01 0.44083147E+01
41 -0.29259329E+02 0.38677175E+01 0.44237640E+01
42 -0.37853065E+02 -0.85937363E+01 0.44244795E+01
43 -0.37837347E+02 0.15718064E-01 0.44243305E+01
44 -0.38882018E+02 -0.10446709E+01 0.44318110E+01
45 -0.33797160E+02 0.50848576E+01 0.44140842E+01
46 -0.36916411E+02 -0.31192503E+01 0.44487774E+01
47 -0.34676425E+02 0.22399861E+01 0.44925774E+01
48 -0.36829201E+02 -0.21527765E+01 0.45105152E+01
49 -0.37217594E+02 -0.38839256E+00 0.45105062E+01
50 -0.37359760E+02 -0.14216608E+00 0.45062330E+01
51 -0.37536431E+02 -0.17667157E+00 0.45008092E+01
52 -0.36651751E+02 0.88468021E+00 0.44974495E+01
53 -0.36361137E+02 0.29061361E+00 0.45913047E+01
54 -0.34596880E+02 0.17642572E+01 0.46529176E+01
55 -0.33484053E+02 0.11128277E+01 0.47028868E+01
56 -0.41992721E+02 -0.85086688E+01 0.48221328E+01
57 -0.36195993E+02 0.57967280E+01 0.49197729E+01
58 -0.37274876E+02 -0.10788826E+01 0.49663271E+01
59 -0.36952990E+02 0.32188543E+00 0.49528268E+01
60 -0.37671640E+02 -0.71864907E+00 0.49807447E+01
61 -0.38447177E+02 -0.77553782E+00 0.49805281E+01
62 -0.38423372E+02 0.23804915E-01 0.49731166E+01
63 -0.37921826E+02 0.50154623E+00 0.49514521E+01
64 -0.37368739E+02 0.55308772E+00 0.51108964E+01
65 -0.39852076E+02 -0.24833377E+01 0.51133664E+01
66 -0.39798119E+02 0.53956895E-01 0.51191947E+01
67 -0.39507245E+02 0.29087405E+00 0.51063872E+01
68 -0.39455095E+02 0.52149807E-01 0.51072388E+01
69 -0.39251442E+02 0.20365394E+00 0.51126149E+01
70 -0.38887611E+02 0.36383031E+00 0.51495471E+01
71 -0.40831054E+02 -0.19434424E+01 0.51374604E+01
72 -0.42618760E+02 -0.17877068E+01 0.51572934E+01
73 -0.39882226E+02 0.27365346E+01 0.51507142E+01
74 -0.39352704E+02 0.52952147E+00 0.51201809E+01
75 -0.41454633E+02 -0.21019288E+01 0.51027874E+01
76 -0.39480703E+02 0.19739299E+01 0.51743206E+01
77 -0.39940530E+02 -0.45982713E+00 0.51938210E+01
78 -0.39901341E+02 0.39189581E-01 0.52062055E+01
79 -0.39582843E+02 0.31849793E+00 0.52081636E+01
80 -0.39117881E+02 0.46496194E+00 0.51958727E+01
81 -0.39304635E+02 -0.18675442E+00 0.51966792E+01
82 -0.39295188E+02 0.94474375E-02 0.51921512E+01
83 -0.39344177E+02 -0.48989268E-01 0.52040830E+01
84 -0.39249618E+02 0.94558626E-01 0.51940255E+01
85 -0.39286211E+02 -0.36592714E-01 0.51454801E+01
86 -0.39823188E+02 -0.53697647E+00 0.51468171E+01
87 -0.34800422E+02 0.50227652E+01 0.51478633E+01
88 -0.34523849E+02 0.27657311E+00 0.51463703E+01
89 -0.34486517E+02 0.37331955E-01 0.51643692E+01
90 -0.36457054E+02 -0.19705367E+01 0.51721366E+01
91 -0.34963031E+02 0.14940233E+01 0.51717206E+01
92 -0.34396285E+02 0.56674589E+00 0.51729476E+01
93 -0.34095371E+02 0.30091400E+00 0.51697836E+01
94 -0.36100713E+02 -0.20053425E+01 0.51696420E+01
95 -0.39099105E+02 -0.29983916E+01 0.51558573E+01
96 -0.34674325E+02 0.44247804E+01 0.51610596E+01
97 -0.39004414E+02 -0.43300891E+01 0.51518375E+01
98 -0.34541134E+02 0.44632799E+01 0.51376275E+01
99 -0.34960872E+02 -0.41973819E+00 0.51360966E+01
100 -0.35080221E+02 -0.11934899E+00 0.51333930E+01
WARNING!
-> SCC is NOT converged, maximal SCC iterations exceeded
--------------------------------------------------------------------------------
DFTB+ running times cpu [s] wall clock [s]
--------------------------------------------------------------------------------
Pre-SCC initialisation + 0.10 ( 0.5%) 0.01 ( 0.3%)
SCC + 18.01 ( 99.0%) 4.97 ( 99.4%)
Post-SCC processing + 0.08 ( 0.5%) 0.02 ( 0.3%)
--------------------------------------------------------------------------------
Missing + 0.00 ( 0.0%) 0.00 ( 0.0%)
Total = 18.20 (100.0%) 5.00 (100.0%)
--------------------------------------------------------------------------------
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
The full input is
Geometry = GenFormat {
38 C
C O H
1 1 -3.2103390000E-01 6.4976606000E-01 6.1134966000E-01
2 1 9.6328881000E-01 2.6810143600E+00 2.4672770000E-02
3 1 3.7008025000E-01 -1.9148818000E-01 -3.4608252000E-01
4 1 1.7062543300E+00 1.8667277800E+00 -9.7432192000E-01
5 1 -4.6635000000E-04 2.0405072500E+00 8.3279825000E-01
6 1 1.3552255700E+00 4.6696619000E-01 -1.1164276800E+00
7 1 -1.2084626700E+00 3.5055440000E-02 1.4611567900E+00
8 1 1.2838829500E+00 4.0436668700E+00 2.3580619000E-01
9 1 1.7368624000E-01 -1.5974433500E+00 -5.6605157000E-01
10 1 2.7167114800E+00 2.5171334100E+00 -1.7385943600E+00
11 1 -6.7994802000E-01 2.7815041000E+00 1.8784723000E+00
12 1 2.1407047300E+00 -2.9303542000E-01 -2.0652228400E+00
13 1 -1.9292987000E+00 7.5069414000E-01 2.4361290700E+00
14 1 6.4765831000E-01 4.7324463100E+00 1.2977432600E+00
15 1 8.3835424000E-01 -2.2447042900E+00 -1.5758687500E+00
16 1 3.4495481300E+00 1.6997917600E+00 -2.6509048200E+00
17 1 -1.6506211100E+00 2.1200052600E+00 2.7154073500E+00
18 1 -3.6777644000E-01 4.1391518900E+00 2.0732747000E+00
19 1 1.9139484800E+00 -1.6634948600E+00 -2.2349815200E+00
20 1 3.1011552300E+00 3.5961796000E-01 -2.8927181400E+00
21 1 -2.4832568600E+00 2.8190296100E+00 3.7147392800E+00
22 1 -1.0551337700E+00 4.8836022000E+00 3.2217757000E+00
23 1 2.5647743600E+00 -2.3565660000E+00 -3.3888315300E+00
24 1 3.8672443600E+00 -3.7443306000E-01 -3.9283627100E+00
25 2 -2.2570870700E+00 4.2401457300E+00 3.7669234400E+00
26 2 3.5670952200E+00 -1.7034416800E+00 -4.2202391900E+00
27 2 -3.4531757200E+00 2.3849873100E+00 4.3012718900E+00
28 2 -8.5119925000E-01 5.9864947800E+00 3.6250608000E+00
29 2 2.2689106300E+00 -3.4863053800E+00 -3.6642365400E+00
30 2 4.8047915300E+00 1.0340452000E-01 -4.5201062700E+00
31 3 -1.3310748400E+00 -1.0903765300E+00 1.3043519700E+00
32 3 2.0065768900E+00 4.5267732800E+00 -4.6496078000E-01
33 3 -7.6392979000E-01 -2.1566928200E+00 -3.6773373000E-01
34 3 2.8953294300E+00 3.6457328500E+00 -1.6719959800E+00
35 3 -2.6358745700E+00 2.0275311000E-01 3.0872061600E+00
36 3 1.0561540100E+00 5.6545207000E+00 1.6511110400E+00
37 3 4.3113722000E-01 -3.2352289900E+00 -1.8495723100E+00
38 3 4.2695602000E+00 2.1622890000E+00 -3.2672901100E+00
}
Driver = VelocityVerlet{
# Possibly should be a bit smaller for real calculations:
TimeStep [fs] = 0.5
# Use the NVE ensemble (as its a molecule, V is infinite)
Thermostat = None {}
# Specify the initial velocities of the atoms to avoid having a 'burn
# in' period to get to a 'typical' microstate
Velocities [AA/ps] { # This is the same unit as xyz format output
0.63060001 10.71652407 0.41599521
-4.78167517 -0.67726160 6.81193886
3.98425977 1.00737908 -10.59008962
-5.00836769 -4.17503533 6.23338156
-6.98937694 -6.67991962 13.49283670
2.60129853 2.94191649 -6.17377828
5.45307788 4.06412641 -12.66174802
-7.65333453 -3.97065257 6.97104050
-10.13358053 2.65525500 1.71478235
2.43208042 7.32942823 4.28579643
-4.30000399 3.49584166 3.08283261
2.24408800 -6.45559687 0.04066731
-1.94541508 3.92663760 -0.72998677
5.60486436 3.94060376 -3.20947636
3.53019985 4.56545155 -1.48062150
7.81517642 2.25960070 4.82188329
-0.50193981 -4.94744725 3.06413849
-0.19059520 4.33561964 2.36256475
0.09466765 -0.51960301 5.72471343
4.47619173 7.41074772 1.11201016
3.27922874 -5.35329287 -2.56702569
3.99264878 -8.45260216 -4.11369388
-1.77619915 -3.53622712 -7.62449802
7.38469860 -1.25504906 0.63982263
-4.58383155 2.77913648 -3.36202315
2.57174728 3.16284242 -2.42263621
-1.51584311 4.83348853 -8.50814642
3.19719689 -5.10152266 4.80391910
-1.82283885 -4.42665140 -0.61092820
0.70148376 -13.29987273 5.73299098
-48.12863500 6.61689320 -3.55300242
-7.79595968 7.24986202 -7.89475790
19.47014048 -24.23046733 -19.62986878
-22.48734706 8.85056458 5.45198051
-8.26315843 12.84226567 -16.40492287
-27.33024406 29.56557052 -25.50583462
-20.88278228 1.24410318 -14.82956937
16.44412954 -1.14851662 13.23381502
}
Steps = 20000 # 10 ps total
MovedAtoms = 1:-1
}
Hamiltonian = xTB {
Method = "GFN2-xTB"
}
Options = {
RandomSeed = 3871906
# speed up a bit by suppressing some file writing
WriteDetailedOut = No
}
Analysis {
# speed up a bit by suppressing some file writing
WriteBandOut = No
}
# This file uses the 5th input format
ParserOptions = {
ParserVersion = 7
}
# if run in MPI parallel, allow openMP threads to be used
Parallel = {
UseOmpThreads = Yes
}
Thanks for reporting. You may have hit the issue reported in #940, which had been fixed already on the main branch. Please try your system with current main and let us know, whether this solves the issue.
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