Monotony error on Output during OpenMX Molecular Dynamics calculation

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Monotony error on Output during OpenMX Molecular Dynamics calculation

Date: 2025/08/10 09:02
Name: Bin Shao <bshao@nankai.edu.cn>: Hello everyone,

I am running a Molecular Dynamics (MD) simulation using OpenMX and encountered a strange repeated error message. The calculation proceeds normally until around MD step 129, SCF step 35, and then I see the following lines repeating:

******************* MD=129 SCF=35 *******************
<Poisson> Poisson's equation using FFT...
<Set_Hamiltonian> Hamiltonian matrix for VNA+dVH+Vxc...
<Cluster> Solving the eigenvalue problem...
Monotony error on Output 2216 2.1719620602164733 -0.46040007661623215E-03
Monotony error on Output 2216 2.1719620602164733 -0.46040007661623215E-03
Monotony error on Output 2216 2.1719620602164733 -0.46040007661623215E-03
(same message keeps repeating)

Calculation type: Molecular Dynamics (MD) simulation

System: 192 atoms SiO

Method: DFT with norm-conserving pseudopotentials

Platform: Ubuntu 20.04, OpenMX 3.9, MPI parallel run

My questions:

What exactly does the Monotony error on Output mean in OpenMX? Is it due to numerical convergence issues or a physical instability in the system?

Could it be related to SCF convergence strategy, e.g., mixing parameters, band broadening, or electronic temperature?

During MD, could changes in atomic positions lead to instability in the Hamiltonian and trigger this error?

Any advice or experience in solving this issue would be greatly appreciated.

Bin Shao

==================================================
#
# The file was generated by the OpenMX Viewer

# Bravais lattice type: NONE
# Reciprocal vector b1 (1/Ang): 0.43877 0.00000 0.00000
# Reciprocal vector b2 (1/Ang): 0.00000 0.43877 0.00000
# Reciprocal vector b3 (1/Ang): 0.00000 0.00000 0.43877

System.CurrrentDirectory ./
System.Name a-SiO2
level.of.stdout 1
level.of.fileout 1

DATA.PATH /home/bshao/proj/openmx/DFT_DATA19

Species.Number 2
<Definition.of.Atomic.Species
O O6.0-s2p2d1 O_PBE19
Si Si7.0-s2p2d1 Si_PBE19
Definition.of.Atomic.Species>

Atoms.Number 192
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 Si -0.01597 -0.06798 0.13356 2.0 2.0
2 Si 0.10282 3.55961 3.50082 2.0 2.0
3 Si 3.77823 3.52630 -0.12898 2.0 2.0
4 Si 3.50363 0.07723 3.64915 2.0 2.0
5 Si 5.22201 1.92533 5.36793 2.0 2.0
6 Si 1.86408 1.85509 1.75416 2.0 2.0
7 Si 1.86222 5.40432 5.35620 2.0 2.0
8 Si 5.37875 5.37227 1.67664 2.0 2.0
9 O 0.94338 1.00093 0.73241 3.0 3.0
10 O 6.03784 2.90234 4.34273 3.0 3.0
11 O 2.91757 4.90920 6.58070 3.0 3.0
12 O 3.89242 5.74239 2.42329 3.0 3.0
13 O 2.40219 6.52894 4.29302 3.0 3.0
14 O 6.68790 4.80827 2.63676 3.0 3.0
15 O 4.33289 3.11821 5.92474 3.0 3.0
16 O 0.80380 4.37959 4.71827 3.0 3.0
17 O 5.69151 6.82564 0.84450 3.0 3.0
18 O 2.29168 0.64246 2.73888 3.0 3.0
19 O 3.07285 2.57236 0.92088 3.0 3.0
20 O 6.04703 0.98142 6.33439 3.0 3.0
21 O 4.02985 1.20536 4.62537 3.0 3.0
22 O 0.98224 6.10201 6.45109 3.0 3.0
23 O 1.21126 3.23488 2.38137 3.0 3.0
24 O 5.20004 4.08532 0.58775 3.0 3.0
25 Si -0.13344 0.14197 7.16337 2.0 2.0
26 Si -0.04539 3.41353 10.84725 2.0 2.0
27 Si 3.57864 3.53146 7.24853 2.0 2.0
28 Si 3.56505 -0.06858 10.69173 2.0 2.0
29 Si 5.45894 1.68473 12.43158 2.0 2.0
30 Si 1.77913 1.86951 9.03904 2.0 2.0
31 Si 1.85260 5.24690 12.58078 2.0 2.0
32 Si 5.51144 5.27509 8.91593 2.0 2.0
33 O 0.60126 1.26213 8.09336 3.0 3.0
34 O 6.59657 2.42518 11.55019 3.0 3.0
35 O 3.19097 4.67513 13.20131 3.0 3.0
36 O 4.78309 6.32695 9.84390 3.0 3.0
37 O 2.38944 6.34803 11.37998 3.0 3.0
38 O 6.30250 4.41070 9.92141 3.0 3.0
39 O 4.19167 2.34600 13.16895 3.0 3.0
40 O 0.82006 4.07390 12.07391 3.0 3.0
41 O 6.14730 6.15335 7.79402 3.0 3.0
42 O 2.30371 0.99097 10.31619 3.0 3.0
43 O 3.02570 2.28001 8.12248 3.0 3.0
44 O 6.30780 0.49621 13.01178 3.0 3.0
45 O 4.60715 0.85832 11.37890 3.0 3.0
46 O 0.91921 5.82901 13.80089 3.0 3.0
47 O 1.01302 3.23054 9.63171 3.0 3.0
48 O 4.69574 4.07207 8.23271 3.0 3.0
49 Si 0.09553 7.07980 0.15518 2.0 2.0
50 Si -0.01891 10.70121 3.72480 2.0 2.0
51 Si 3.61029 10.81638 -0.03739 2.0 2.0
52 Si 3.62087 7.08823 3.40674 2.0 2.0
53 Si 5.30186 8.84728 5.37386 2.0 2.0
54 Si 1.89749 9.04381 1.88397 2.0 2.0
55 Si 1.69933 12.62586 5.46902 2.0 2.0
56 Si 5.21179 12.70931 1.69176 2.0 2.0
57 O 1.44946 7.87931 0.79854 3.0 3.0
58 O 6.02007 9.75188 4.29090 3.0 3.0
59 O 2.73459 11.63707 6.09861 3.0 3.0
60 O 4.81907 13.69044 2.95151 3.0 3.0
61 O 2.70984 13.49219 4.61908 3.0 3.0
62 O 6.22504 11.44212 2.24231 3.0 3.0
63 O 4.49040 10.03399 6.14914 3.0 3.0
64 O 0.92117 11.87503 4.30321 3.0 3.0
65 O 6.23501 13.60807 0.84572 3.0 3.0
66 O 3.05299 8.53622 2.93650 3.0 3.0
67 O 2.67776 10.36520 1.26347 3.0 3.0
68 O 6.07392 8.45569 6.79240 3.0 3.0
69 O 4.93100 7.44651 4.41344 3.0 3.0
70 O 1.16443 13.72424 6.47649 3.0 3.0
71 O 0.51359 9.58716 2.58000 3.0 3.0
72 O 4.02777 12.35634 0.54721 3.0 3.0
73 Si -0.11696 6.99402 7.08803 2.0 2.0
74 Si 0.04535 10.54506 10.61876 2.0 2.0
75 Si 3.58588 10.88663 7.18388 2.0 2.0
76 Si 3.70011 7.20004 10.64741 2.0 2.0
77 Si 5.55990 9.13325 12.51906 2.0 2.0
78 Si 1.89230 8.86039 8.77569 2.0 2.0
79 Si 1.73384 12.28803 12.43915 2.0 2.0
80 Si 5.48090 12.50946 8.79271 2.0 2.0
81 O 0.88852 7.83723 8.07018 3.0 3.0
82 O 5.47784 10.53480 11.53046 3.0 3.0
83 O 2.43433 10.92091 13.09382 3.0 3.0
84 O 4.73157 13.68398 9.60629 3.0 3.0
85 O 2.96100 13.10494 11.72356 3.0 3.0
86 O 6.86379 12.09222 9.75246 3.0 3.0
87 O 4.69819 9.50671 13.97531 3.0 3.0
88 O 0.82922 11.87462 11.17734 3.0 3.0
89 O 6.18126 12.78439 7.36475 3.0 3.0
.......
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
14.3200000 0.0000000 0.0000000
0.0000000 14.3200000 0.0000000
0.0000000 0.0000000 14.3200000
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.energycutoff 150.0
scf.maxIter 100
scf.EigenvalueSolver cluster
scf.Kgrid 1 1 1
scf.criterion 5.0e-6

#scf.EigenvalueSolver DC
#orderN.HoppingRanges 7.0
#orderN.NumHoppings 3
#orderN.Method Recursion

MD.Type NVT_NH
MD.TimeStep 1.0
MD.maxIter 1000
NH.Mass.HeatBath 20.0

<MD.TempControl
4
1 1178.392
200 3000.0
600 1000.0
1000 300.0
MD.TempControl>

#MD.Type NVT_NH
#MD.TimeStep 1.0 # fs
#MD.maxIter 1000
#NH.Mass.HeatBath 30.0
#
#<MD.TempControl
# 4
# 1 3000.0
# 200 3000.0
# 600 1000.0
# 1000 300.0
#MD.TempControl>

scf.restart on
=====================================================

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Re: Monotony error on Output during OpenMX Molecular Dynamics calculation ( No.1 )

Date: 2025/08/26 22:30
Name: Kazume NISHIDATE <nisidate@iwate-u.ac.jp>

Dear Bin Shao,

The “Atom.Number” is 192, while only 89 atoms were listed in your input file, which means no one can reproduce your error.

Here is my personal advice, based on my experience.
There are two strategies to solve the problem.

1) Increase the cutoff energy and perform the same calculation. It will change the values of the matrix elements in the eigenvalue problem, and that may lead to a solvable matrix problem.

2) Change the algorithm to solve the eigenvalue problem.
You are currently using the ‘cluster’ algorithm as in your input file.
scf.EigenvalueSolver cluster

Of course, you can try both of the above simultaneously.

西館数芽
Kazume NISHIDATE Ph.D

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishidate@gmail.com, nisidate@iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/

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