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A trouble with generation of restart file
Date: 2021/11/14 22:21
Name: Takuma Takeda

Dear OpenMX forum members;

I found a trouble with generating restart files in structural optimization.

Calculational Condition: OpenMX3.9 running on MateriApps Live! (Windows 10)
CPU:AMD Ryzen

Input file: I put it below.
*)Fractional coordination was generated from SeeKPath(https://www.materialscloud.org/work/tools/seekpath).

When I run structural optimization and generate restart file (*.dat#),
I found the coordinates were not successfully written in restart. Calculation itself was normally done.
As I have checked, it seemed that some columns from the start coordinate in input file were included, and some of parameters such as electron's number of spin (up/down).

I am sorry not to presume the reason and check reproducibility in other condition, but might to be in the coordinates, defined by minus value (if all coordinates are positive, as I have conducted previous in another calculation, there was no trouble).

I would happy to know how to avoid this trouble.

Your Sincerely,

Input file
#Sorry, I changed some Hubbard value from my original condition. However I think there is no relation, because I found the same trouble in the case of without DFT+U.#
System.CurrrentDirectory ./
System.Name disp01
level.of.stdout 1
level.of.fileout 1

Species.Number 2
<Definition.of.Atomic.Species #precise
O O6.0-s3p2d2 O_PBE19
Ti Ti7.0-s3p2d2f1 Ti_PBE19
Definition.of.Atomic.Species>

<Hubbard.U.values #eV
O 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 1d 0.0 2d 0.0
Ti 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 1d 5.0 2d 0.0 1f 0.0
Hubbard.U.values>

Atoms.Number 16
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 Ti 0.1280000000 -0.1280000000 0.0440000000 6.0 6.0 on
2 Ti 0.8720000000 0.1280000000 0.9560000000 6.0 6.0 on
3 Ti 0.7786000000 0.2214000000 0.2669000000 6.0 6.0 on
4 Ti 0.2214000000 -0.2214000000 0.7331000000 6.0 6.0 on
5 Ti 0.0538000000 -0.0538000000 0.3659000000 6.0 6.0 on
6 Ti 0.9462000000 0.0538000000 0.6341000000 6.0 6.0 on
7 O 0.6760000000 0.3240000000 0.0600000000 3.0 3.0 on
8 O 0.3240000000 -0.3240000000 0.9400000000 3.0 3.0 on
9 O 0.2410000000 -0.2410000000 0.2450000000 3.0 3.0 on
10 O 0.7590000000 0.2410000000 0.7550000000 3.0 3.0 on
11 O 0.5880000000 0.4120000000 0.3450000000 3.0 3.0 on
12 O 0.4120000000 -0.4120000000 0.6550000000 3.0 3.0 on
13 O 0.9530000000 0.0470000000 0.1580000000 3.0 3.0 on
14 O 0.0470000000 -0.0470000000 0.8420000000 3.0 3.0 on
15 O 0.8660000000 0.1340000000 0.4410000000 3.0 3.0 on
16 O 0.1340000000 -0.1340000000 0.5590000000 3.0 3.0 on
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
4.87600000000000 1.90100000000000 0.00000000000000
-4.87600000000000 1.90100000000000 0.00000000000000
-0.27455449109500 0.00000000000000 10.14643606656500
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.Hubbard.U on # on|off, default=off
scf.DFTU.Type 1 # 1:Simplified(Dudarev)|2:General, default=1
scf.dc.Type sFLL
scf.ElectronicTemperature 300.0
scf.energycutoff 500
scf.maxIter 1000
scf.EigenvalueSolver band
scf.Kgrid 7 7 3
scf.Mixing.Type rmm-diis
scf.Init.Mixing.Weight 0.0010
scf.Min.Mixing.Weight 0.0001
scf.Max.Mixing.Weight 0.3
scf.Mixing.History 30
scf.Mixing.StartPulay 15
scf.Mixing.EveryPulay 1
scf.criterion 3.67e-6
scf.stress.tensor on
scf.restart on

MD.Type opt
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 10 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 5
MD.TimeStep 1.0
MD.Opt.criterion 7.35e-4
<MD.Fixed.Cell.Vectors
0 0 1
0 0 1
0 1 0
MD.Fixed.Cell.Vectors>

geoopt.restart on
###############################################################################
Generated restart file#########################################################
System.CurrrentDirectory ./
System.Name disp01
level.of.stdout 1
level.of.fileout 1
Species.Number 2
<Definition.of.Atomic.Species #precise
O O6.0-s3p2d2 O_PBE19
Ti Ti7.0-s3p2d2f1 Ti_PBE19
Definition.of.Atomic.Species>



<Hubbard.U.values #eV
O 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 1d 0.0 2d 0.0
Ti 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 1d 5.0 2d 0.0 1f 0.0
Hubbard.U.values>

Atoms.Number 16
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates

1 Ti 0.1280000000 -0.1280000000 0.0440000000 0.12635671094454 -0.12635670257685 0.04299195393179 2 Ti 0.8720000000 0.1280000000 0.9560000000 0.87364328571588 0.12635670245106 0.95700804424470 3 Ti 0.7786000000 0.2214000000 0.2669000000 0.78166738111535 0.21833262434449 0.26818123015040 4 Ti 0.2214000000 -0.2214000000 0.7331000000 0.21833262021617 -0.21833262576908 0.73181878041406 5 Ti 0.0538000000 -0.0538000000 0.3659000000 0.05379619777730 -0.05379618071204 0.36864713522961 6 Ti 0.9462000000 0.0538000000 0.6341000000 0.94620381099114 0.05379618195020 0.63135286755763 7 O 0.6760000000 0.3240000000 0.0600000000 0.67720513502725 0.32279486742307 0.06109029818474 8 O 0.3240000000 -0.3240000000 0.9400000000 0.32279486728251 -0.32279486413831 0.93890970232656 9 O 0.2410000000 -0.2410000000 0.2450000000 0.23883234160884 -0.23883235930609 0.24402947545197 10 O 0.7590000000 0.2410000000 0.7550000000 0.76116765460809 0.23883235835199 0.75597052062903 11 O 0.5880000000 0.4120000000 0.3450000000 0.58962727520646 0.41037272140009 0.34450363399968 12 O 0.4120000000 -0.4120000000 0.6550000000 0.41037272379385 -0.41037272256429 0.65549636622765 13 O 0.9530000000 0.0470000000 0.1580000000 0.95271470295820 0.04728529635556 0.15713871338227 14 O 0.0470000000 -0.0470000000 0.8420000000 0.04728529627895 -0.04728529549497 0.84286128045275 15 O 0.8660000000 0.1340000000 0.4410000000 0.86673087290925 0.13326912654699 0.43962738960820 16 O 0.1340000000 -0.1340000000 0.5590000000 0.13326912256249 -0.13326912650308 0.56037261006997Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
4.876000000000000 1.901000000000000 0.000000000000000
-4.876000000000000 1.901000000000000 0.000000000000000
-0.274554491095000 0.000000000000000 10.146436066564998
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.Hubbard.U on # on|off, default=off
scf.DFTU.Type 1 # 1:Simplified(Dudarev)|2:General, default=1
scf.dc.Type sFLL
scf.ElectronicTemperature 300.0
scf.energycutoff 500
scf.maxIter 1000
scf.EigenvalueSolver band
scf.Kgrid 7 7 3
scf.Mixing.Type rmm-diis
scf.Init.Mixing.Weight 0.0010
scf.Min.Mixing.Weight 0.0001
scf.Max.Mixing.Weight 0.3
scf.Mixing.History 30
scf.Mixing.StartPulay 15
scf.Mixing.EveryPulay 1
scf.criterion 3.67e-6
scf.stress.tensor on
scf.restart on


MD.Type opt
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 10 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 5
MD.TimeStep 1.0
MD.Opt.criterion 7.35e-4
<MD.Fixed.Cell.Vectors
0 0 1
0 0 1
0 1 0
MD.Fixed.Cell.Vectors>




geoopt.restart on


scf.fixed.grid 0.00000000000000 0.00000000000000 0.00000000000000


MD.Current.Iter 3


<Atoms.Unitvectors.Velocity
0.0000000000000000000000 0.0000000000000000000000 0.0000000000000000000000
0.0000000000000000000000 0.0000000000000000000000 0.0000000000000000000000
0.0000000000000000000000 0.0000000000000000000000 0.0000000000000000000000
Atoms.Unitvectors.Velocity>


<NPT.WV.F0
0.0000000000000000000000 0.0000000000000000000000 0.0000000000000000000000
0.0000000000000000000000 0.0000000000000000000000 0.0000000000000000000000
0.0000000000000000000000 0.0000000000000000000000 0.0000000000000000000000
NPT.WV.F0>
###############################################################################
メンテ
Page: [1]

Re: A trouble with generation of restart file ( No.1 )
Date: 2021/11/15 02:11
Name: Naoya Yamaguchi

Hi,

Your issue seems to be the same as reported in
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2122 .

If it is true, you can resolve it by avoiding the tab characters.
When I calculated your input by copying the above, it worked normally.

Regards,
Naoya Yamaguchi
メンテ
Re: A trouble with generation of restart file ( No.2 )
Date: 2021/11/15 23:01
Name: Takuma Takeda

Dear Dr.Yamaguchi,

I appreciate for your prompt advise, and apologize not for searching forum's log thoroughly.

Surely, I have checked my input file on MateriAppsLive, and found some tab was included.
I succeeded in solving this problem by deleting tab and restart was generated normally.

I will have to edit an input file carefully.

Your Sincerely,
メンテ

Page: [1]

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