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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

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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 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 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 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 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 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 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> 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 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

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