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Geometry optimization of metal slab yields nan forces
Date: 2018/06/07 23:09
Name: Dechamps Samuel   <samuel.dechamps@uclouvain.be>

Dear Openmx community,

I have an issue regarding a geometry optimization (GO) of a slab made of a metal.
I consider different metals, i.e. Ag Al Au Cr Cu Pd Pt Ti, composing a slab of 9 atoms along the fcc [111] direction. On top of it are 4 layers of graphene.

However, for the cases of Ag, Cu, Ti, I get 'nan' forces after the first self-consistent cycle for the atom at the end of the slab (opposite to graphene). This obviously makes the GO of such systems impossible.

I already tried to passivate this atom with :
-an empty atom : EAg Ag7.0_GGA-s2p2d1 E
-an hydrogen atom : H H0_GGA-s2p1 H0_GGA

and I also allowed this metal atom to relax with :
<MD.Fixed.XYZ
1 1 1 0
...
MD.Fixed.XYZ>

Thanks in advance,
S. Dechamps

------------------------------------------------------------------------------------------

This yields :

Species.Number 2
<Definition.of.Atomic.Species
C C5.0_GGA-s2p2d1 C5.0_GGA
Ag Ag7.0_GGA-s2p2d1 Ag7.0_GGA
Definition.of.Atomic.Species>

Atoms.Number 17
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Ag 1.6974097914175 2.94 0.0 8.5 8.5
2 Ag 0.84870489570875 1.47 2.4004999479275146 8.5 8.5
3 Ag 0.000000000000 0.0000 4.800999895855029 8.5 8.5
4 Ag 1.6974097914175 2.94 7.201499843782544 8.5 8.5
5 Ag 0.84870489570875 1.47 9.601999791710059 8.5 8.5
6 Ag 0.000000000000 0.0000 12.002499739637575 8.5 8.5
7 Ag 1.6974097914175 2.94 14.402999687565089 8.5 8.5
8 Ag 0.84870489570875 1.47 16.803499635492603 8.5 8.5
9 Ag 0.000000000000 0.0000 19.203999583420117 8.5 8.5
10 C 0.000000000000 0.0000 21.703999583420117 2.0 2.0
11 C 0.84870489570875 1.47 21.703999583420117 2.0 2.0
12 C 0.84870489570875 1.47 25.05399958342012 2.0 2.0
13 C 1.6974097914175 2.94 25.05399958342012 2.0 2.0
14 C 0.000000000000 0.0000 28.403999583420116 2.0 2.0
15 C 0.84870489570875 1.47 28.403999583420116 2.0 2.0
16 C 0.84870489570875 1.47 31.753999583420118 2.0 2.0
17 C 1.6974097914175 2.94 31.753999583420118 2.0 2.0
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
2.5461146871262494 1.47 0.0
0.00000000000 2.94 0.0
0.00000000000 0.0 100.0
Atoms.UnitVectors>

MD.Type Opt # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 7 # default=7
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 200 # default=1
MD.Opt.criterion 2.0e-3 # default=1.0e-4 (Hartree/bohr)

<MD.Fixed.XYZ
1 1 1 1
2 1 1 1
3 1 1 1
4 1 1 1
5 1 1 1
6 1 1 1
7 1 1 1
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
17 1 1 0
MD.Fixed.XYZ>

------------------------------------------------------------------------------------------

with the error in the *.md (and subsequently in *.out) :

17
time= 0.000 (fs) Energy= -1073.30952 (Hartree) Cell_Vectors= 2.54611 1.47000 0.00000 0.00000 2.94000 0.00000 0.00000 0.00000 100.00000
Ag 1.69741 2.94000 0.00000 nan nan nan 0.00000 0.00000 0.00000 -0.03614 0.00000 0.00000 0.00000
Ag 0.84870 1.47000 2.40050 0.00001 0.00002 0.00096 0.00000 0.00000 0.00000 0.02681 0.00000 0.00000 0.00000
Ag 0.00000 0.00000 4.80100 -0.00000 -0.00000 -0.00039 0.00000 0.00000 0.00000 0.00799 0.00000 0.00000 0.00000
Ag 1.69741 2.94000 7.20150 0.00000 0.00000 -0.00019 0.00000 0.00000 0.00000 0.00126 0.00000 0.00000 0.00000
Ag 0.84870 1.47000 9.60200 -0.00000 -0.00000 -0.00004 0.00000 0.00000 0.00000 0.00003 0.00000 0.00000 0.00000
Ag 0.00000 0.00000 12.00250 -0.00000 -0.00000 -0.00017 0.00000 0.00000 0.00000 0.00021 0.00000 0.00000 0.00000
Ag 1.69741 2.94000 14.40300 0.00000 0.00000 0.00003 0.00000 0.00000 0.00000 -0.00499 0.00000 0.00000 0.00000
Ag 0.84870 1.47000 16.80350 -0.00001 -0.00001 0.00267 0.00000 0.00000 0.00000 0.02839 0.00000 0.00000 0.00000
Ag 0.00000 0.00000 19.20400 -0.00004 -0.00001 -0.00115 0.00000 0.00000 0.00000 -0.11758 0.00000 0.00000 0.00000
C 0.00000 0.00000 21.70400 -0.00007 0.00004 -0.00136 0.00000 0.00000 0.00000 0.04276 0.00000 0.00000 0.00000
C 0.84870 1.47000 21.70400 0.00009 -0.00004 0.00531 0.00000 0.00000 0.00000 0.06200 0.00000 0.00000 0.00000
C 0.84870 1.47000 25.05400 -0.00011 -0.00003 -0.00026 0.00000 0.00000 0.00000 0.04548 0.00000 0.00000 0.00000
C 1.69741 2.94000 25.05400 0.00011 0.00003 -0.00055 0.00000 0.00000 0.00000 -0.05320 0.00000 0.00000 0.00000
C 0.00000 0.00000 28.40400 -0.00013 -0.00006 -0.00009 0.00000 0.00000 0.00000 -0.04958 0.00000 0.00000 0.00000
C 0.84870 1.47000 28.40400 0.00012 0.00006 -0.00002 0.00000 0.00000 0.00000 0.04750 0.00000 0.00000 0.00000
C 0.84870 1.47000 31.75400 -0.00012 -0.00004 -0.00082 0.00000 0.00000 0.00000 0.02332 0.00000 0.00000 0.00000
C 1.69741 2.94000 31.75400 0.00012 0.00005 -0.00016 0.00000 0.00000 0.00000 -0.02424 0.00000 0.00000 0.00000



メンテ
Page: [1]

Re: Geometry optimization of metal slab yields nan forces ( No.1 )
Date: 2018/06/08 13:27
Name: Naoya Yamaguchi

Hi,

I have some questions about your calculation:

1. For PAO and VPS, Are "C5.0_GGA-s2p2d1", "C5.0_GGA", "Ag7.0_GGA-s2p2d1", and "Ag7.0_GGA" prepared by your self, not included in the directory "DFT_DATA13"?

2. Is the SCF calculation normally finished? Could you show its history, and the keywords about SCF in your input file?

Regards,
Naoya Yamaguchi
メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.2 )
Date: 2018/06/08 20:36
Name: Dechamps Samuel  <samuel.dechamps@uclouvain.be>

Dear Naoya Yamaguchi,

regarding your questions :

1) I used the same PAO and VPS as in the DFT_DATA13 repository, I just named them differently.

2) It is normally finished. Please take a look at it below.

Best,
S. Dechamps

***********************************************************
***********************************************************
SCF history at MD= 1
***********************************************************
***********************************************************

SCF= 1 NormRD= 1.000000000000 Uele= -157.030677610901
SCF= 2 NormRD= 587.250270845273 Uele= -257.941326324643
SCF= 3 NormRD= 584.436716099630 Uele= -257.103277485013
SCF= 4 NormRD= 104.842049015098 Uele= -189.086656279504
SCF= 5 NormRD= 18.895964461705 Uele= -176.645441531867
SCF= 6 NormRD= 26.405182460302 Uele= -180.525763538560
SCF= 7 NormRD= 20.329120671430 Uele= -179.370824939511
SCF= 8 NormRD= 7.834168646629 Uele= -176.783548657565
SCF= 9 NormRD= 5.255749165374 Uele= -175.353021463772
SCF= 10 NormRD= 4.264510756915 Uele= -175.075169480556
SCF= 11 NormRD= 3.010222850435 Uele= -174.113624207802
SCF= 12 NormRD= 2.797628128096 Uele= -173.408086351463
SCF= 13 NormRD= 2.005939480975 Uele= -172.704883989537
SCF= 14 NormRD= 0.769992003774 Uele= -170.620692190936
SCF= 15 NormRD= 1.697793719420 Uele= -166.687260711360
SCF= 16 NormRD= 0.242801191321 Uele= -165.903530462952
SCF= 17 NormRD= 0.397228006079 Uele= -164.018744331776
SCF= 18 NormRD= 0.303881302718 Uele= -164.062349325477
SCF= 19 NormRD= 0.222907310764 Uele= -163.763610326068
SCF= 20 NormRD= 0.200212534814 Uele= -163.763823802553
SCF= 21 NormRD= 0.150285837262 Uele= -163.777564100214
SCF= 22 NormRD= 0.135356018211 Uele= -163.807921727345
SCF= 23 NormRD= 0.115647532247 Uele= -163.857567942058
SCF= 24 NormRD= 0.083233300971 Uele= -163.893817684133
SCF= 25 NormRD= 0.059142560824 Uele= -163.931878335433
SCF= 26 NormRD= 0.042235387458 Uele= -163.948764918169
SCF= 27 NormRD= 0.028317741724 Uele= -163.970687682889
SCF= 28 NormRD= 0.016007264679 Uele= -163.988100863363
SCF= 29 NormRD= 0.007642444016 Uele= -163.999773796803
SCF= 30 NormRD= 0.003578703020 Uele= -164.006087927022
SCF= 31 NormRD= 0.002476895839 Uele= -164.007409505923
SCF= 32 NormRD= 0.001239537641 Uele= -164.009305778704
SCF= 33 NormRD= 0.000603517575 Uele= -164.010370246211
SCF= 34 NormRD= 0.000249900004 Uele= -164.010946128663
SCF= 35 NormRD= 0.000011438143 Uele= -164.011353980249
SCF= 36 NormRD= 0.000003711352 Uele= -164.011378522803
SCF= 37 NormRD= 0.000007773141 Uele= -164.011389084918
SCF= 38 NormRD= 0.000004131196 Uele= -164.011384378324
SCF= 39 NormRD= 0.000001714344 Uele= -164.011382012457
SCF= 40 NormRD= 0.000000708284 Uele= -164.011380764264
SCF= 41 NormRD= 0.000000102623 Uele= -164.011380013455
SCF= 42 NormRD= 0.000000031196 Uele= -164.011379878002
SCF= 43 NormRD= 0.000000003780 Uele= -164.011379839536
SCF= 44 NormRD= 0.000000003381 Uele= -164.011379838937
メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.3 )
Date: 2018/06/08 20:48
Name: Dechamps Samuel  <samuel.dechamps@uclouvain.be>

Please find here the keywords :

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.SpinOrbit.Coupling off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 900.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.Kgrid 36 36 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 50 # default=5
scf.Mixing.StartPulay 5 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
scf.lapack.dste dstevx # dstevx|dstedc|dstegr,default=dstevx
scf.restart off
メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.4 )
Date: 2018/06/09 01:38
Name: Naoya Yamaguchi

Dear S. Dechamps,

I tried the calculation using an input file that is made by modifying your input slightly. Then, the SCF calculation is normally finished, and the behavior is also so normal that all values for the atomic forces are finite, not "nan".

I guess from your original input that the problem is caused by a wrong solution for the SCF calculation, that is, wrong electronic states that might be obtained, and the solution for it may be to increase the value for the keyword "scf.Mixing.StartPulay".

I leave the modified input, and the md file and the SCF history that were obtained actually:

Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p2d1 C_PBE13
Ag Ag7.0-s2p2d1 Ag_PBE13
Definition.of.Atomic.Species>

Atoms.Number 17
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Ag 1.6974097914175 2.94 0.0 8.5 8.5
2 Ag 0.84870489570875 1.47 2.4004999479275146 8.5 8.5
3 Ag 0.000000000000 0.0000 4.800999895855029 8.5 8.5
4 Ag 1.6974097914175 2.94 7.201499843782544 8.5 8.5
5 Ag 0.84870489570875 1.47 9.601999791710059 8.5 8.5
6 Ag 0.000000000000 0.0000 12.002499739637575 8.5 8.5
7 Ag 1.6974097914175 2.94 14.402999687565089 8.5 8.5
8 Ag 0.84870489570875 1.47 16.803499635492603 8.5 8.5
9 Ag 0.000000000000 0.0000 19.203999583420117 8.5 8.5
10 C 0.000000000000 0.0000 21.703999583420117 2.0 2.0
11 C 0.84870489570875 1.47 21.703999583420117 2.0 2.0
12 C 0.84870489570875 1.47 25.05399958342012 2.0 2.0
13 C 1.6974097914175 2.94 25.05399958342012 2.0 2.0
14 C 0.000000000000 0.0000 28.403999583420116 2.0 2.0
15 C 0.84870489570875 1.47 28.403999583420116 2.0 2.0
16 C 0.84870489570875 1.47 31.753999583420118 2.0 2.0
17 C 1.6974097914175 2.94 31.753999583420118 2.0 2.0
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
2.5461146871262494 1.47 0.0
0.00000000000 2.94 0.0
0.00000000000 0.0 100.0
Atoms.UnitVectors>

MD.Type Opt # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 7 # default=7
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 200 # default=1
MD.Opt.criterion 2.0e-3 # default=1.0e-4 (Hartree/bohr)

<MD.Fixed.XYZ
1 1 1 1
2 1 1 1
3 1 1 1
4 1 1 1
5 1 1 1
6 1 1 1
7 1 1 1
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
17 1 1 0
MD.Fixed.XYZ>

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.SpinOrbit.Coupling off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 150.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.Kgrid 12 12 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.01 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.1 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)
scf.lapack.dste dstevx # dstevx|dstedc|dstegr,default=dstevx
scf.restart off

---

17
time= 0.000 (fs) Energy= -1073.30818 (Hartree) Cell_Vectors= 2.54611 1.47000 0.00000 0.00000 2.94000 0.00000 0.00000 0.00000 100.00000
Ag 1.69741 2.94000 0.00000 0.00004 0.00005 -0.00171 0.00000 0.00000 0.00000 -0.01799 0.00000 0.00000 0.00000
Ag 0.84870 1.47000 2.40050 0.00001 0.00002 0.00118 0.00000 0.00000 0.00000 0.01189 0.00000 0.00000 0.00000
Ag 0.00000 0.00000 4.80100 -0.00002 -0.00004 -0.00105 0.00000 0.00000 0.00000 0.00671 0.00000 0.00000 0.00000
Ag 1.69741 2.94000 7.20150 -0.00003 -0.00004 0.00075 0.00000 0.00000 0.00000 -0.00123 0.00000 0.00000 0.00000
Ag 0.84870 1.47000 9.60200 0.00004 0.00007 0.00042 0.00000 0.00000 0.00000 0.00115 0.00000 0.00000 0.00000
Ag 0.00000 0.00000 12.00250 -0.00002 -0.00003 -0.00026 0.00000 0.00000 0.00000 -0.00199 0.00000 0.00000 0.00000
Ag 1.69741 2.94000 14.40300 0.00005 0.00008 0.00075 0.00000 0.00000 0.00000 0.00070 0.00000 0.00000 0.00000
Ag 0.84870 1.47000 16.80350 -0.00002 -0.00004 0.00364 0.00000 0.00000 0.00000 0.01392 0.00000 0.00000 0.00000
Ag 0.00000 0.00000 19.20400 -0.00009 -0.00008 -0.00349 0.00000 0.00000 0.00000 -0.01576 0.00000 0.00000 0.00000
C 0.00000 0.00000 21.70400 -0.00156 -0.00261 0.00017 0.00000 0.00000 0.00000 0.01258 0.00000 0.00000 0.00000
C 0.84870 1.47000 21.70400 0.00155 0.00255 0.00290 0.00000 0.00000 0.00000 -0.00022 0.00000 0.00000 0.00000
C 0.84870 1.47000 25.05400 -0.00021 -0.00027 -0.00013 0.00000 0.00000 0.00000 0.02172 0.00000 0.00000 0.00000
C 1.69741 2.94000 25.05400 0.00026 0.00037 -0.00043 0.00000 0.00000 0.00000 -0.02891 0.00000 0.00000 0.00000
C 0.00000 0.00000 28.40400 -0.00009 -0.00007 -0.00011 0.00000 0.00000 0.00000 -0.02527 0.00000 0.00000 0.00000
C 0.84870 1.47000 28.40400 0.00005 0.00001 -0.00003 0.00000 0.00000 0.00000 0.02381 0.00000 0.00000 0.00000
C 0.84870 1.47000 31.75400 -0.00013 -0.00013 -0.00009 0.00000 0.00000 0.00000 0.01191 0.00000 0.00000 0.00000
C 1.69741 2.94000 31.75400 0.00015 0.00017 -0.00033 0.00000 0.00000 0.00000 -0.01304 0.00000 0.00000 0.00000

---

***********************************************************
***********************************************************
SCF history at MD= 1
***********************************************************
***********************************************************

SCF= 1 NormRD= 1.000000000000 Uele= -152.629469238843
SCF= 2 NormRD= 9.174612306564 Uele= -145.931477622716
SCF= 3 NormRD= 9.101678152963 Uele= -145.960619797416
SCF= 4 NormRD= 4.337341010660 Uele= -147.813400815802
SCF= 5 NormRD= 2.715603825523 Uele= -148.920230437665
SCF= 6 NormRD= 2.150941258799 Uele= -149.868923752100
SCF= 7 NormRD= 1.902876877010 Uele= -150.658564751815
SCF= 8 NormRD= 1.701226991050 Uele= -151.385393236399
SCF= 9 NormRD= 1.517986931948 Uele= -152.051529661656
SCF= 10 NormRD= 1.360862456384 Uele= -152.647094335057
SCF= 11 NormRD= 1.227431247857 Uele= -153.182702489390
SCF= 12 NormRD= 1.111077780467 Uele= -153.671213706721
SCF= 13 NormRD= 1.005350374103 Uele= -154.119609308732
SCF= 14 NormRD= 0.907915072033 Uele= -154.529374000648
SCF= 15 NormRD= 0.819652289455 Uele= -154.900825440121
SCF= 16 NormRD= 0.740973391325 Uele= -155.236327846340
SCF= 17 NormRD= 0.671090740411 Uele= -155.539759556808
SCF= 18 NormRD= 0.608788229900 Uele= -155.815001111749
SCF= 19 NormRD= 0.552921736504 Uele= -156.065294922100
SCF= 20 NormRD= 0.502459956177 Uele= -156.293180189833
SCF= 21 NormRD= 3.357145137035 Uele= -163.412778100608
SCF= 22 NormRD= 0.117628661315 Uele= -158.481420187132
SCF= 23 NormRD= 1.022601913622 Uele= -159.059788321020
SCF= 24 NormRD= 0.107794811238 Uele= -158.713977680027
SCF= 25 NormRD= 0.139141260910 Uele= -160.775614863355
SCF= 26 NormRD= 0.106325986638 Uele= -160.556674533239
SCF= 27 NormRD= 0.086095171626 Uele= -160.969402685209
SCF= 28 NormRD= 0.069787660236 Uele= -161.289800024363
SCF= 29 NormRD= 0.032859801825 Uele= -161.651365821091
SCF= 30 NormRD= 0.028493368054 Uele= -161.676247199794
SCF= 31 NormRD= 0.026347278971 Uele= -161.671657718498
SCF= 32 NormRD= 0.018230424260 Uele= -161.650553209787
SCF= 33 NormRD= 0.014986857284 Uele= -161.634934717416
SCF= 34 NormRD= 0.009792909501 Uele= -161.595651266298
SCF= 35 NormRD= 0.006427204552 Uele= -161.571809474755
SCF= 36 NormRD= 0.002972137269 Uele= -161.551802462839
SCF= 37 NormRD= 0.000939295581 Uele= -161.540388773598
SCF= 38 NormRD= 0.000187913776 Uele= -161.536939100633
SCF= 39 NormRD= 0.000121178463 Uele= -161.536271682152
SCF= 40 NormRD= 0.000041721776 Uele= -161.537071241370
SCF= 41 NormRD= 0.000007075785 Uele= -161.537227677873
SCF= 42 NormRD= 0.000009349380 Uele= -161.537366259579
SCF= 43 NormRD= 0.000007149247 Uele= -161.537340229393
SCF= 44 NormRD= 0.000004749478 Uele= -161.537323002653
SCF= 45 NormRD= 0.000001353577 Uele= -161.537300571595
SCF= 46 NormRD= 0.000000609699 Uele= -161.537296669969
SCF= 47 NormRD= 0.000000125755 Uele= -161.537293637302
SCF= 48 NormRD= 0.000000041228 Uele= -161.537293250410
SCF= 49 NormRD= 0.000000011865 Uele= -161.537293103103
SCF= 50 NormRD= 0.000000007227 Uele= -161.537293197793
SCF= 51 NormRD= 0.000000002489 Uele= -161.537293203127

*******************************************************
Total energy (Hartree) at MD = 1
*******************************************************

Uele. -161.537293203127

Ukin. 477.008371052992
UH0. -12050.611279133436
UH1. 0.346281434502
Una. -351.185907860285
Unl. -114.660111871210
Uxc0. -79.022090116386
Uxc1. -79.022090116386
Ucore. 11123.838651069394
Uhub. 0.000000000000
Ucs. 0.000000000000
Uzs. 0.000000000000
Uzo. 0.000000000000
Uef. 0.000000000000
UvdW 0.000000000000
Utot. -1073.308175540815

Note:

Utot = Ukin+UH0+UH1+Una+Unl+Uxc0+Uxc1+Ucore+Uhub+Ucs+Uzs+Uzo+Uef+UvdW

Uene: band energy
Ukin: kinetic energy
UH0: electric part of screened Coulomb energy
UH1: difference electron-electron Coulomb energy
Una: neutral atom potential energy
Unl: non-local potential energy
Uxc0: exchange-correlation energy for alpha spin
Uxc1: exchange-correlation energy for beta spin
Ucore: core-core Coulomb energy
Uhub: LDA+U energy
Ucs: constraint energy for spin orientation
Uzs: Zeeman term for spin magnetic moment
Uzo: Zeeman term for orbital magnetic moment
Uef: electric energy by electric field
UvdW: semi-empirical vdW energy

(see also PRB 72, 045121(2005) for the energy contributions)



Chemical potential (Hartree) -0.143691135949


I changed the values for the keywords "scf.energycutoff", "scf.Kgrid", and "scf.criterion" to reduce the computational time for the test, so you can use appropriate ones.

Regards,
Naoya Yamaguchi
メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.5 )
Date: 2018/06/11 21:12
Name: Dechamps Samuel  <samuel.dechamps@uclouvain.be>

Dear Naoya Yamaguchi,

thank you for your answer.
Oddly enough, for the case of Silver, it worked on another machine (with the same parameters as the ones given above).

Nevertheless, the problem remains for Ti and Cu.

Let's take the case of Ti :

When adding empty atoms at the edge :

Species.Number 3
<Definition.of.Atomic.Species
C C5.0_GGA-s2p2d1 C5.0_GGA
Ti Ti7.0_PBE-s2p2d1 Ti7.0_PBE
Ti_ea Ti7.0_PBE-s2p2d1 E
Definition.of.Atomic.Species>

Atoms.Number 18
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Ti_ea 0.000000000000 0.0000 -2.3727390641759722 0.0 0.0
2 Ti_ea 1.6777798822650527 2.906 0.0000000000000000 0.0 0.0
3 Ti_ea 0.8388899411325264 1.453 2.3727390641759722 0.0 0.0
4 Ti 0.000000000000 0.0000 4.7454781283519445 6.0 6.0
5 Ti 1.6777798822650527 2.906 7.118217192527917 6.0 6.0
6 Ti 0.8388899411325264 1.453 9.490956256703889 6.0 6.0
7 Ti 0.000000000000 0.0000 11.863695320879861 6.0 6.0
8 Ti 1.6777798822650527 2.906 14.236434385055833 6.0 6.0
9 Ti 0.8388899411325264 1.453 16.609173449231807 6.0 6.0
10 Ti 0.000000000000 0.0000 18.981912513407778 6.0 6.0
11 C 0.000000000000 0.0000 20.981912513407778 2.0 2.0
12 C 0.8388899411325264 1.453 20.981912513407778 2.0 2.0
13 C 0.8388899411325264 1.453 24.33191251340778 2.0 2.0
14 C 1.6777798822650527 2.906 24.33191251340778 2.0 2.0
15 C 0.000000000000 0.0000 27.681912513407777 2.0 2.0
16 C 0.8388899411325264 1.453 27.681912513407777 2.0 2.0
17 C 0.8388899411325264 1.453 31.03191251340778 2.0 2.0
18 C 1.6777798822650527 2.906 31.03191251340778 2.0 2.0
Atoms.SpeciesAndCoordinates>

I get the following output (in *.out and *.md respectively) :

<coordinates.forces
18
1 E 0.00000 0.00000 -2.37274 0.000000003070 0.000000005345 0.000017284096
2 E 1.67778 2.90600 0.00000 -0.000000004509 -0.000000007714 0.000055973505
3 E 0.83889 1.45300 2.37274 0.000000126024 0.000000218948 0.000190238544
4 Ti 0.00000 0.00000 4.74548 nan nan nan
5 Ti 1.67778 2.90600 7.11822 nan nan nan
6 Ti 0.83889 1.45300 9.49096 nan nan nan
7 Ti 0.00000 0.00000 11.86370 nan nan nan
8 Ti 1.67778 2.90600 14.23643 nan nan nan
9 Ti 0.83889 1.45300 16.60917 nan nan nan
10 Ti 0.00000 0.00000 18.98191 nan nan nan
11 C 0.00000 0.00000 20.98191 nan nan nan
12 C 0.83889 1.45300 20.98191 nan nan nan
13 C 0.83889 1.45300 24.33191 nan nan nan
14 C 1.67778 2.90600 24.33191 nan nan nan
15 C 0.00000 0.00000 27.68191 nan nan nan
16 C 0.83889 1.45300 27.68191 nan nan nan
17 C 0.83889 1.45300 31.03191 nan nan nan
18 C 1.67778 2.90600 31.03191 nan nan nan
coordinates.forces>

18
time= 0.000 (fs) Energy= -461.45064 (Hartree) Cell_Vectors= 2.51667 1.45300 0.00000 0.00000 2.90600 0.00000 0.00000 0.00000 100.00000
E 0.00000 0.00000 -2.37274 0.00000 0.00000 0.00002 0.00000 0.00000 0.00000 -0.00016 0.00000 0.00000 0.00000
E 1.67778 2.90600 0.00000 -0.00000 -0.00000 0.00006 0.00000 0.00000 0.00000 -0.00244 0.00000 0.00000 0.00000
E 0.83889 1.45300 2.37274 0.00000 0.00000 0.00019 0.00000 0.00000 0.00000 -0.00781 0.00000 0.00000 0.00000
Ti 0.00000 0.00000 4.74548 0.00035 0.00005 0.00477 0.00000 0.00000 0.00000 -0.01136 0.00000 0.00000 0.00000
Ti 1.67778 2.90600 7.11822 0.00005 0.00009 -0.00925 0.00000 0.00000 0.00000 0.02299 0.00000 0.00000 0.00000
Ti 0.83889 1.45300 9.49096 -0.00001 -0.00001 0.00049 0.00000 0.00000 0.00000 -0.00160 0.00000 0.00000 0.00000
Ti 0.00000 0.00000 11.86370 0.00005 0.00008 -0.00049 0.00000 0.00000 0.00000 -0.00066 0.00000 0.00000 0.00000
Ti 1.67778 2.90600 14.23643 -0.00005 -0.00009 0.00301 0.00000 0.00000 0.00000 0.00200 0.00000 0.00000 0.00000
Ti 0.83889 1.45300 16.60917 0.00006 0.00010 -0.00976 0.00000 0.00000 0.00000 0.01584 0.00000 0.00000 0.00000
Ti 0.00000 0.00000 18.98191 -0.00009 -0.00015 -0.00840 0.00000 0.00000 0.00000 0.07773 0.00000 0.00000 0.00000
C 0.00000 0.00000 20.98191 -0.00013 -0.00008 0.03584 0.00000 0.00000 0.00000 -0.02508 0.00000 0.00000 0.00000
C 0.83889 1.45300 20.98191 -0.00018 0.00007 -0.01475 0.00000 0.00000 0.00000 -0.07088 0.00000 0.00000 0.00000
C 0.83889 1.45300 24.33191 -0.00012 -0.00005 0.00012 0.00000 0.00000 0.00000 0.04808 0.00000 0.00000 0.00000
C 1.67778 2.90600 24.33191 0.00011 0.00004 -0.00062 0.00000 0.00000 0.00000 -0.04692 0.00000 0.00000 0.00000
C 0.00000 0.00000 27.68191 -0.00011 -0.00004 -0.00002 0.00000 0.00000 0.00000 -0.04708 0.00000 0.00000 0.00000
C 0.83889 1.45300 27.68191 0.00011 0.00004 -0.00003 0.00000 0.00000 0.00000 0.04753 0.00000 0.00000 0.00000
C 0.83889 1.45300 31.03191 -0.00011 -0.00005 -0.00077 0.00000 0.00000 0.00000 0.02320 0.00000 0.00000 0.00000
C 1.67778 2.90600 31.03191 0.00012 0.00005 -0.00020 0.00000 0.00000 0.00000 -0.02336 0.00000 0.00000 0.00000

Which is even weirder for me.

I'm currently asking myself several questions :
1) Why is there nan in the *.out and not in the *.md ?
2) If the nan does not come from edge problem, why is causing it ?

Hoping that you'll be able to help me with those,
Best regards,
S. Dechamps



メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.6 )
Date: 2018/06/11 22:41
Name: T. Ozaki

Dear Dechamps,

Could you show us the full input file for Ti?
(I could't reproduce your problem)

Regards,

TO
メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.7 )
Date: 2018/06/11 23:35
Name: Dechamps Samuel  <samuel.dechamps@uclouvain.be>

Dear Ozaki-sensei,

please find here the input file for Ti :


#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name Ti-Gr
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

data.path /home/sam/Software/openmx3.8/DFT_DATA13_clusters/

#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
C C5.0_GGA-s2p2d1 C5.0_GGA
Ti Ti7.0_PBE-s2p2d1 Ti7.0_PBE
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 17
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Ti 1.6777798822650527 2.906 0.0 6.0 6.0
2 Ti 0.8388899411325264 1.453 2.3727390641759722 6.0 6.0
3 Ti 0.000000000000 0.0000 4.7454781283519445 6.0 6.0
4 Ti 1.6777798822650527 2.906 7.118217192527917 6.0 6.0
5 Ti 0.8388899411325264 1.453 9.490956256703889 6.0 6.0
6 Ti 0.000000000000 0.0000 11.863695320879861 6.0 6.0
7 Ti 1.6777798822650527 2.906 14.236434385055833 6.0 6.0
8 Ti 0.8388899411325264 1.453 16.609173449231807 6.0 6.0
9 Ti 0.000000000000 0.0000 18.981912513407778 6.0 6.0
10 C 0.000000000000 0.0000 20.981912513407778 2.0 2.0
11 C 0.8388899411325264 1.453 20.981912513407778 2.0 2.0
12 C 0.8388899411325264 1.453 24.33191251340778 2.0 2.0
13 C 1.6777798822650527 2.906 24.33191251340778 2.0 2.0
14 C 0.000000000000 0.0000 27.681912513407777 2.0 2.0
15 C 0.8388899411325264 1.453 27.681912513407777 2.0 2.0
16 C 0.8388899411325264 1.453 31.03191251340778 2.0 2.0
17 C 1.6777798822650527 2.906 31.03191251340778 2.0 2.0
Atoms.SpeciesAndCoordinates>


Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
2.516669823397579 1.453 0.0
0.00000000000 2.906 0.0
0.00000000000 0.0 100.0
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.SpinOrbit.Coupling off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 500.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.Kgrid 36 36 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 50 # default=5
scf.Mixing.StartPulay 5 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
scf.lapack.dste dstevx # dstevx|dstedc|dstegr,default=dstevx
scf.restart off

#
# vdW
#

scf.dftD on
version.dftD 3
DFTD3.damp zero
DFTD.IntDirection 1 1 0

#
# MD or Geometry Optimization
#

MD.Type EF # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 7 # default=7
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 200 # default=200
MD.maxIter 200 # default=1
MD.Opt.criterion 2.0e-3 # default=1.0e-4 (Hartree/bohr)

<MD.Fixed.XYZ
1 1 1 1
2 1 1 1
3 1 1 1
4 1 1 1
5 1 1 1
6 1 1 1
7 1 1 1
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
17 1 1 0
MD.Fixed.XYZ>
メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.8 )
Date: 2018/06/12 10:02
Name: T. Ozaki

Dear Dechamps,

Thank you for sharing your input file.
It turned out that the problem is caused by division by zero in a routine,
Total_Energy.c, when the DFT-D3 method is used.

I have fixed the problem, and released a patch 3.8.5 at
http://www.openmx-square.org/download.html

After applying the patch, I could get the convergent result.
The following is the input and output files.
https://t-ozaki.issp.u-tokyo.ac.jp/openmx-files/Ti-Gr.dat
https://t-ozaki.issp.u-tokyo.ac.jp/openmx-files/Ti-Gr.out

Please take a look at these files.
Thank you for your report again.

Best regards,

TO



メンテ
Re: Geometry optimization of metal slab yields nan forces ( No.9 )
Date: 2018/06/12 23:39
Name: Dechamps Samuel  <samuel.dechamps@uclouvain.be>

Dear Ozaki-sensei,

after applying the patch, it works.

Many thanks for your quick response.

Best,
S. Dechamps
メンテ

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