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Constrained optimization
Date: 2018/03/16 11:26
Name: Hashmi   <arqumhashmi@gmail.com>

I am doing structure optimization, just relaxing the atomic positions, where x and y is fixed and i want to optimized z coordinates.
So i tried Constrained relaxation and included MD.Fixed.XYZ, but after optimization i saw that in
relaxed structure x and y is little bit displaced as well like

X Y X Y
0.666666666 0.666666666 transforms to 0.66795708977843 0.66864275470611
1.000000000 0.333333333 0.99894530189225 0.33370858639809

The x and y shouldn't be change even little bit because it is fixed. Is it normal?? or i did something wrong??

Please just give a comment on it.
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Page: [1]

Re: Constrained optimization ( No.1 )
Date: 2018/03/21 05:43
Name: Chi-Cheng Lee  <cclee.physics@gmail.com>

Hi, Hashmi,

Could it be that there is a typo for "<MD.Fixed.XYZ" or "MD.Fixed.XYZ>" in your input file?
Maybe it will be helpful if you can copy that part of input file here.

Cheers,
Chi-Cheng
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Re: Constrained optimization ( No.2 )
Date: 2018/03/22 14:28
Name: Hashmi  <arqumhashmi@gmail.com>

Species.Number 3
<Definition.of.Atomic.Species
Se Se7.0-s2p2d1 Se_PBE13
Mn Mn8.0-s3p2d2f1 Mn_PBE13
Definition.of.Atomic.Species>

Atoms.Number 16
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 Se 0.66707437490900 0.66930946726612 0.16639556712945 3.0 3.0 off
2 Se 0.32913867787673 0.00027093129895 0.39559542316156 3.0 3.0 off
3 Se 0.33038161721844 -0.00250441563942 0.16689373498955 3.0 3.0 off
4 Se -0.00004544126731 0.32872816653460 0.39603319364295 3.0 3.0 off
5 Se 1.00280318090372 0.33275545601191 0.16655222089333 3.0 3.0 off
6 Se 0.67135559610282 0.67133176660645 0.39549621043000 3.0 3.0 off
7 Se 0.99933584450708 0.66282707060885 0.04873344030352 3.0 3.0 off
8 Se 0.66786978676606 -0.00151279336836 0.28014657948851 3.0 3.0 off
9 Se 0.33616423510276 0.33544634662001 0.05007893788585 3.0 3.0 off
10 Se 1.00073037024674 0.66904605892015 0.28049859111788 3.0 3.0 off
11 Se 0.66475986389182 0.00056404706345 0.05068061276237 3.0 3.0 off
12 Se 0.33207136791968 0.33274100581309 0.28216507543494 3.0 3.0 off
13 Mn 0.00266968613895 -0.00406930561958 0.10464690489555 6.0 9.0 on
14 Mn 0.67047284153634 0.33107842257451 0.33619472685655 6.0 9.0 on
15 Mn 0.66980716334484 0.33900378066085 0.10605506623188 9.0 6.0 on
16 Mn 0.33298581827446 0.67228797501581 0.33518999624598 9.0 6.0 on
Atoms.SpeciesAndCoordinates>

<MD.Fixed.XYZ
1 1 1 0
2 1 1 0
3 1 1 0
4 1 1 0
5 1 1 0
6 1 1 0
7 1 1 0
8 1 1 0
9 1 1 0
10 1 1 0
11 1 1 0
12 1 1 0
13 1 1 0
14 1 1 0
15 1 1 0
16 1 1 0
MD.Fixed.XYZ>

Atoms.UnitVectors.Unit AU
<Atoms.UnitVectors
12.117490164245517 0.000000000000000 0.000000000000000
-6.058745082028272 10.494054312225355 0.000000000000000
0.000000000000000 0.000000000000000 56.691779657367697
Atoms.UnitVectors>

scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp zero # zero|bj, default=bj
DFTD.Unit AU # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 0 # default=1 1 1 (1:on 0:off)

scf.Electric.Field 0.0 0.0 0.6 # default=0.0 0.0 0.0 (GV/m)

<Hubbard.U.values # eV
Se 1s 0.0 2s 0.0 1p 0.0 2p 0.0 1d 0.0
Mn 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>
scf.Hubbard.U On # On|Off, default=off
scf.Hubbard.Occupation dual # onsite|full|dual
scf.partialCoreCorrection On # On|Off

# MD or Geometry Optimization
MD.Type RF # Opt|DIIS|BFGS|RF|EF
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 500 # default=1
MD.Opt.criterion 5.0e-5 # default=0.0003 (Hartree/Bohr)


#scf.restart on
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization ON # On|Off|NC
#scf.SpinOrbit.Coupling ON # On|Off, default=off
#scf.Constraint.NC.Spin ON # On|Off, default=off
scf.ElectronicTemperature 400.0 # default=300 (K)
scf.energycutoff 420.0 # default=150 (Ry)
scf.maxIter 55 # default=40
scf.EigenvalueSolver Band # Recursion|Cluster|Band
scf.Kgrid 7 7 1 # means 4x4x4
scf.Mixing.Type Rmm-Diis # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.100 # default=0.30
scf.Min.Mixing.Weight 0.0005 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 15 # default=5
scf.Mixing.StartPulay 35 # default=6
scf.criterion 3.7e-6 # default=1.0e-6 (Hartree)
メンテ
Re: Constrained optimization ( No.3 )
Date: 2018/03/22 14:32
Name: Hashmi  <arqumhashmi@gmail.com>

System.CurrrentDirectory ./
System.Name MnPSe
level.of.stdout 1
level.of.fileout 1

Species.Number 2
<Definition.of.Atomic.Species
Se Se7.0-s2p2d1 Se_PBE13
Mn Mn8.0-s3p2d2f1 Mn_PBE13
P P7.0-s2p2d1 P_PBE13
Definition.of.Atomic.Species>

Atoms.Number 16
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 Se 0.66707437490900 0.66930946726612 0.16639556712945 3.0 3.0 off
2 Se 0.32913867787673 0.00027093129895 0.39559542316156 3.0 3.0 off
3 Se 0.33038161721844 -0.00250441563942 0.16689373498955 3.0 3.0 off
4 Se -0.00004544126731 0.32872816653460 0.39603319364295 3.0 3.0 off
5 Se 1.00280318090372 0.33275545601191 0.16655222089333 3.0 3.0 off
6 Se 0.67135559610282 0.67133176660645 0.39549621043000 3.0 3.0 off
7 Se 0.99933584450708 0.66282707060885 0.04873344030352 3.0 3.0 off
8 Se 0.66786978676606 -0.00151279336836 0.28014657948851 3.0 3.0 off
9 Se 0.33616423510276 0.33544634662001 0.05007893788585 3.0 3.0 off
10 Se 1.00073037024674 0.66904605892015 0.28049859111788 3.0 3.0 off
11 Se 0.66475986389182 0.00056404706345 0.05068061276237 3.0 3.0 off
12 Se 0.33207136791968 0.33274100581309 0.28216507543494 3.0 3.0 off
13 Mn 0.00266968613895 -0.00406930561958 0.10464690489555 6.0 9.0 on
14 Mn 0.67047284153634 0.33107842257451 0.33619472685655 6.0 9.0 on
15 Mn 0.66980716334484 0.33900378066085 0.10605506623188 9.0 6.0 on
16 Mn 0.33298581827446 0.67228797501581 0.33518999624598 9.0 6.0 on
Atoms.SpeciesAndCoordinates>

<MD.Fixed.XYZ
1 1 1 0
2 1 1 0
3 1 1 0
4 1 1 0
5 1 1 0
6 1 1 0
7 1 1 0
8 1 1 0
9 1 1 0
10 1 1 0
11 1 1 0
12 1 1 0
13 1 1 0
14 1 1 0
15 1 1 0
MD.Fixed.XYZ>

Atoms.UnitVectors.Unit AU
<Atoms.UnitVectors
12.117490164245517 0.000000000000000 0.000000000000000
-6.058745082028272 10.494054312225355 0.000000000000000
0.000000000000000 0.000000000000000 56.691779657367697
Atoms.UnitVectors>

scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp zero # zero|bj, default=bj
DFTD.Unit AU # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 0 # default=1 1 1 (1:on 0:off)

scf.Electric.Field 0.0 0.0 0.6 # default=0.0 0.0 0.0 (GV/m)

<Hubbard.U.values # eV
Se 1s 0.0 2s 0.0 1p 0.0 2p 0.0 1d 0.0
Mn 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>
scf.Hubbard.U On # On|Off, default=off
scf.Hubbard.Occupation dual # onsite|full|dual
scf.partialCoreCorrection On # On|Off

# MD or Geometry Optimization
MD.Type RF # Opt|DIIS|BFGS|RF|EF
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 500 # default=1
MD.Opt.criterion 5.0e-5 # default=0.0003 (Hartree/Bohr)


#scf.restart on
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization ON # On|Off|NC
#scf.SpinOrbit.Coupling ON # On|Off, default=off
#scf.Constraint.NC.Spin ON # On|Off, default=off
scf.ElectronicTemperature 400.0 # default=300 (K)
scf.energycutoff 420.0 # default=150 (Ry)
scf.maxIter 55 # default=40
scf.EigenvalueSolver Band # Recursion|Cluster|Band
scf.Kgrid 7 7 1 # means 4x4x4
scf.Mixing.Type Rmm-Diis # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.100 # default=0.30
scf.Min.Mixing.Weight 0.0005 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 15 # default=5
scf.Mixing.StartPulay 35 # default=6
scf.criterion 3.7e-6 # default=1.0e-6 (Hartree)


This is my input file. I have included +U and Electric field as well. Is something wrong here??
メンテ
Re: Constrained optimization ( No.4 )
Date: 2018/03/22 15:05
Name: Chi-Cheng Lee  <cclee.physics@gmail.com>

Dear Hashmi,

The use of MD.Fixed.XYZ looks good to me.
But I didn't see 0.666666666 0.666666666 ...
Let me make sure that you began with 0.666666666 0.666666666
in the input file (say, case.dat), and then the input file was updated to
the one you have posted (case.dat#)?

Regards,
Chi-Cheng
メンテ
Re: Constrained optimization ( No.5 )
Date: 2018/03/22 16:05
Name: Hashmi  <arqumhashmi@gmail.com>

Atoms.Number 16
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 Se 0.666666666 0.666666666 0.181940004 3.0 3.0 off
2 Se 0.333333333 1.000000002 0.431879997 3.0 3.0 off
3 Se 0.333333333 0.000000000 0.181940004 3.0 3.0 off
4 Se 0.000000000 0.333333333 0.431879997 3.0 3.0 off
5 Se 1.000000000 0.333333333 0.181940004 3.0 3.0 off
6 Se 0.666666666 0.666666666 0.431879997 3.0 3.0 off
7 Se 1.000000000 0.666666666 0.068000004 3.0 3.0 off
8 Se 0.666666666 0.000000000 0.317940027 3.0 3.0 off
9 Se 0.333333333 0.333333333 0.068000004 3.0 3.0 off
10 Se 1.000000000 0.666666666 0.317940027 3.0 3.0 off
11 Se 0.666666666 0.000000000 0.068000004 3.0 3.0 off
12 Se 0.333333333 0.333333333 0.317940027 3.0 3.0 off
13 Mn 0.000000000 0.000000000 0.125200003 6.0 9.0 on
14 Mn 0.666666666 0.333333333 0.375140011 6.0 9.0 on
15 Mn 0.666666666 0.333333333 0.124750003 9.0 6.0 on
16 Mn 0.333333333 0.666666666 0.374689996 9.0 6.0 on
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
6.4123001099 0.0000000000 0.0000000000
-3.2061500549 5.5532147918 0.0000000000
0.0000000000 0.0000000000 30.0000000000
Atoms.UnitVectors>

I started with this input.
メンテ
Re: Constrained optimization ( No.6 )
Date: 2018/03/22 16:29
Name: Chi-Cheng Lee  <cclee.physics@gmail.com>

Dear Hashmi,

I couldn't see anything wrong for the issue of fixing atomic positions.
Maybe someone else could provide a better solution.
But I am wondering whether you can really run the input file, for example,
the number of species (2) is inconsistent with the species you have listed (3).

Species.Number 2
<Definition.of.Atomic.Species
Se Se7.0-s2p2d1 Se_PBE13
Mn Mn8.0-s3p2d2f1 Mn_PBE13
P P7.0-s2p2d1 P_PBE13
Definition.of.Atomic.Species>

Regards,
Chi-Cheng

メンテ
Re: Constrained optimization ( No.7 )
Date: 2018/03/23 01:21
Name: T. Ozaki

Hi,

Did you apply the patch for OpenMX Ver. 3.8?

The original of Ver. 3.8 has a bug that the constraint scheme by the keyword 'MD.Fixed.XYZ'
does not work properly for the EF and RF optimizers. The bug will be fixed by applying the
patch as explained at
http://www.openmx-square.org/bugfixed/18Mar05/README.txt

Regards,

TO
メンテ
Re: Constrained optimization ( No.8 )
Date: 2018/03/23 11:36
Name: Hashmi  <arqumhashmi@gmail.com>

Anyway thanks a lot for your help Chi-Cheng.
Sorry that is my mistake (Copy paste mistake).
yeah that's inconsistent but i am using correct info in original input.



Prof. Ozaki Thanks a lot and yes you are right. this was the problem with RF.
i didn't apply the patch and that was the problem.
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