Problem in optimizing the absorption

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Problem in optimizing the absorption

Date: 2025/01/22 05:21
Name: atefeh <atefeharefi@gmail.com>: Hello everyone
I have prepared the following file to optimize the structure of nanotubes with zwitterionic amino acids.
Species.Number 5
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE19
C C6.0-s2p2d1 C_PBE19
N N6.0-s2p2d1 N_PBE19
O O6.0-s2p2d1 O_PBE19
Si Si7.0-s2p2d1 Si_PBE19
Definition.of.Atomic.Species>
......
Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
29.999999999999989 0.000000000000000 0.000000000000000
0.000000000000000 29.999999999999989 0.000000000000000
0.000000000000000 0.000000000000000 21.599799999999988
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 30
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 1 1 2
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7
scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp bj # zero|bj, default=bj
DFTD.Unit Ang # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)

MD.Type optc5
MD.maxIter 200
MD.TimeStep 1.0
MD.Opt.criterion 0.0003

But after some time, it stops running with the following error.
******************* MD=11 SCF=48 *******************
<Poisson> Poisson's equation using FFT...
<Set_Hamiltonian> Hamiltonian matrix for VNA+dVH+Vxc...
<Band> Solving the eigenvalue problem...
KGrids1: 0.00000
KGrids2: 0.00000
KGrids3: -0.37500 -0.12500 0.12500 0.37500

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 1456398 RUNNING AT SCI-LAB04-C06.SAD.UM.AC.IR
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 1456399 RUNNING AT SCI-LAB04-C06.SAD.UM.AC.IR
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================

I would appreciate your guidance.

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Re: Problem in optimizing the absorption ( No.1 )

Date: 2025/01/23 19:17
Name: Yung-Ting Lee

Parameters listed below is good for your system:
scf.energycutoff 300
MD.Type opt

--

(1) 30 Ry for energy cutoff is low. Enough grid is required for integrals.

(2)
opt is for structure optimization only
Reference: https://www.openmx-square.org/openmx_man3.9/node49.html

optc5 is for variable-cell optimization
Reference: https://www.openmx-square.org/openmx_man3.8/node56.html

Re: Problem in optimizing the absorption ( No.2 )

Date: 2025/01/26 04:26
Name: atefeh <atefeharefi@gmail.com>

Hello dear
Thanks for your attention
The instructions you provided were applied to the input file.
....

Species.Number 5
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE19
C C6.0-s2p2d1 C_PBE19
N N6.0-s2p2d1 N_PBE19
O O6.0-s2p2d1 O_PBE19
Si Si7.0-s2p2d1 Si_PBE19
Definition.of.Atomic.Species>

Atoms.Number 138
Atoms.SpeciesAndCoordinates.Unit Ang
.....
Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
30.800000000000001 0.000000000000000 0.000000000000000
0.000000000000000 30.800000000000001 0.000000000000000
0.000000000000000 0.000000000000000 21.599799999999995
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 300
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 1 1 2
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7
scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp bj # zero|bj, default=bj
DFTD.Unit Ang # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)

MD.Type opt
MD.maxIter 300
MD.TimeStep 1.0
MD.Opt.criterion 0.0003

But the result is as follows.
Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.080789082911
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.047744794910
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.036181166623
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.034098026412
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.025945907998
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.119414149496
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.168778513381
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.117337906952
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.139244740918
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.030149183123
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.017891535975
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.015178420831
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.013198127538
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.009524949003
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.008021183601
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.008658900890
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.010480816803
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.061389260976
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.143357818703
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.110241495265
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.084364520923
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.299844827157
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.077470143299
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.098737982999
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.125137068746
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.015163333996
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004619696267
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004338961705
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004307232453
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004246241417
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004230406506
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004184083452
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004211013150
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.006943166476
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.046760503707
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.119271249524
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.092403714380
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.075377490510
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.061333538428
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.053593383387
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.045805646540
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.152331041846
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.137343949424
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.144381381027
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.025064359108
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.007995055466
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004475249004
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004442785556
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004436415550
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004435041314
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004469583018
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004486937877
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004518331459
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004545229839
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.007044164443
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.045140594236
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.134380069808
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.109366103893
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.032426418265
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.007923647228
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004741323801
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004666370940
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004669815896
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004698005354
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004635868977
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.009276260850
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.044227965102
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.089002802351
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.045299424804
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.017235636073
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.008074288299
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004649707275
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004534578181
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004633527626
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.011600501412
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.030739464795
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.026010354951
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.020449361796
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.017260398374
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.013454226713
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.011771326237
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.042709839557
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.053521446354
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004497238853
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004375279699
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004346173562
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004303074226
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004355671113
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.005649048284
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.033961133515
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.080942736065
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.054816024888
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.042205966567
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.173851394462
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.137503372571
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.033759695697
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.008144466342
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004445663191
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004172559688
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003968463859
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004108227256
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.016713831578
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.102003604711
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.177090233551
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.072102449878
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.039532704939
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.027428209412
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.021205924180
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.014805417945
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.048933897632
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.056919023722
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.009129291032
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003834515932
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003711396701
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003807154877
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004546643505
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.006540944518
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.039451196633
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.102910628788
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.075543583365
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.044665054876
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.128552269536
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.130498137018
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.126185068632
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.030116664345
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.006848924047
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003639346535
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003577412250
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003548331486
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003507443516
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003498821442
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003488363667
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003482612561
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.003503385934
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.006775259055

Can increasing the X and Y dimensions of the unit cell solve the problem?
'I don't have access to strong computing resources.'

Re: Problem in optimizing the absorption ( No.3 )

Date: 2025/01/27 22:22
Name: Yung-Ting Lee

A. Usually, when force convergence doesn't reach, I will update the atomic coordinates in the last step and restart the DFT calculation for optimization.

The newest coordinates will be stored in *.dat#.

(1) Type in:
--------------------------------
cp filename.dat# filename.dat
--------------------------------

(2)
remove a commend in the new filename.dat (in the last line).
--------------------------------
MD.Current.Iter 300
--------------------------------

(3) Add a command line for restarting the calculation by using electron density saved in the folder "namefile_rev".
--------------------------------
scf.restart on
--------------------------------

(4) Restart the calculation for optimization again.

B. On the other hand, please check the optimized structure stored in namefile.md.

"Drag and drop" this md file to OpenMX Viewer in the browser, you can examine the optimization process of the structure and check if the total energy is decreasing.

Re: Problem in optimizing the absorption ( No.4 )

Date: 2025/01/30 03:50
Name: atefeh <atefeharefi@gmail.com>

Hello
Thanks for your attention
I followed the steps you guided me to. I ran the program again. I only had one value.
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.004436415550

Is it calculated correctly or not?

Another issue, the zwitterionic glycine molecule in the structure was converted to a non-zwitterionic molecule.
(In the initial structure of glycine with nanotube, 3 hydrogen atoms are connected to the nitrogen atom, but after the program is finished, one of the hydrogens is separated from the nitrogens and bonded to oxygen.)

Re: Problem in optimizing the absorption ( No.5 )

Date: 2025/01/31 17:51
Name: Yung-Ting Lee

It may not be correct to restart the calculation of optimization.

Please check the references about "restart":
[1] https://www.openmx-square.org/openmx_man3.5/node31.html
[2] https://www.openmx-square.org/openmx_man3.9/node52.html

Re: Problem in optimizing the absorption ( No.6 )

Date: 2025/01/31 18:18
Name: dena <daa58768199@gmail.com>

Thank you very much for your response.
I think it's my mistake that the file name ;System.Name ; is not the same as the command file name in the terminal. I'll try it and post the result for others. to use.
What should I do if the glycine type doesn't change?Please!

Re: Problem in optimizing the absorption ( No.7 )

Date: 2025/01/31 19:54
Name: atefeh <atefeharefi@gmail.com>

hello dear
Thank you for your attention. I will study and inform after doing.

Re: Problem in optimizing the absorption ( No.8 )

Date: 2025/02/03 16:48
Name: atefeh <atefeharefi@gmail.com>

Hello dear
The naming error has been corrected. The problem has been resolved.
But I had another question: Is it appropriate to use the method for optimization like my structure?
If the answer is yes, could you guide me on how to set the parameters correctly?

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