Problem with NEB restart and with specifying path |
- Date: 2015/07/23 21:28
- Name: Mauro Sgroi
<maurofrancesco.sgroi@gmail.com>
- Dear developers,
I've the following problem with Openmx 3.7.
If I restart a NEB calculation or try to specify manually the NEB path, I get the following error:
Format error for NEB1.Atoms.SpeciesAndCoordinates
My input file is below.
Thanks a lot and best regards,
Mauro Sgroi.
System.CurrrentDirectory /net/manager/remote/qespresso/limnpo4_NEB/
System.Name limnpo4_NEB
DATA.PATH /data5/sgroi/DATABASE/DFT_DATA13
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (1-3)
#
# flag of memory leak checker
#
memory.leak on # on|off, default=off
#
# Definition of Atomic Species
#
Species.Number 4
<Definition.of.Atomic.Species
Li Li8.0-s3p3d2 Li_PBE13
Mn Mn6.0-s3p3d3 Mn_PBE13
P P7.0-s3p3d2f1 P_PBE13
O O5.0-s2p2d1 O_PBE13
Definition.of.Atomic.Species>
<Hubbard.U.values # eV
Li 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 3p 0.0 1d 0.0 2d 0.0
Mn 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 3p 0.0 1d 4.5 2d 0.0 3d 0.0
P 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 3p 0.0 1d 0.0 2d 0.0 1f 0.0
O 1s 0.0 2s 0.0 1p 0.0 2p 0.0 1d 0.0
Hubbard.U.values>
#
# Atoms
#
Atoms.Number 55
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 Mn 2.96953 1.56110 4.63756 10.0 5.0 on
2 Mn 2.94904 7.65668 4.62937 10.0 5.0 on
3 Mn 7.58201 10.74383 0.12063 10.0 5.0 on
4 Mn 7.56152 4.57240 0.11243 10.0 5.0 on
5 Mn 2.32857 10.73363 2.25411 10.0 5.0 on
6 Mn 2.33892 4.59731 2.26890 10.0 5.0 on
7 Mn 8.19213 1.53620 2.48110 10.0 5.0 on
8 Mn 8.20248 7.66687 2.49589 10.0 5.0 on
9 P 0.97361 1.53572 1.97650 2.5 2.5 on
10 P 0.96267 7.66236 1.96654 2.5 2.5 on
11 P 9.56838 10.73815 2.78346 2.5 2.5 on
12 P 9.55743 4.59778 2.77350 2.5 2.5 on
13 P 4.28083 10.72472 4.34741 2.5 2.5 on
14 P 4.26765 4.63828 4.34691 2.5 2.5 on
15 P 6.26340 1.49522 0.40309 2.5 2.5 on
16 P 6.25022 7.67579 0.40259 2.5 2.5 on
17 O 1.01886 1.52935 3.52368 3.0 3.0 on
18 O 1.00426 7.66475 3.51328 3.0 3.0 on
19 O 9.52678 10.73576 1.23672 3.0 3.0 on
20 O 9.51219 4.60415 1.22632 3.0 3.0 on
21 O 4.22014 10.70545 1.14077 3.0 3.0 on
22 O 4.15748 4.74490 1.12637 3.0 3.0 on
23 O 6.37356 1.38860 3.62363 3.0 3.0 on
24 O 6.31090 7.69506 3.60923 3.0 3.0 on
25 O 4.80637 1.47018 0.92091 3.0 3.0 on
26 O 4.79606 7.67996 0.97392 3.0 3.0 on
27 O 5.73499 10.72055 3.77608 3.0 3.0 on
28 O 5.72467 4.66332 3.82909 3.0 3.0 on
29 O 0.48953 10.72046 3.36923 3.0 3.0 on
30 O 0.47517 4.61336 3.36311 3.0 3.0 on
31 O 10.05588 1.52014 1.38688 3.0 3.0 on
32 O 10.04151 7.68005 1.38077 3.0 3.0 on
33 O 8.79670 5.82602 3.43178 3.0 3.0 on
34 O 8.84402 11.98590 3.44322 3.0 3.0 on
35 O 1.68703 6.41461 1.30678 3.0 3.0 on
36 O 1.73434 0.30748 1.31822 3.0 3.0 on
37 O 6.99772 6.43438 1.05582 3.0 3.0 on
38 O 7.00329 0.26206 1.13110 3.0 3.0 on
39 O 3.52776 5.87145 3.61889 3.0 3.0 on
40 O 3.53333 11.96613 3.69417 3.0 3.0 on
41 O 3.53537 9.48625 3.68049 3.0 3.0 on
42 O 3.42426 3.43022 3.76696 3.0 3.0 on
43 O 6.99567 8.91426 1.06950 3.0 3.0 on
44 O 7.10679 2.70329 0.98304 3.0 3.0 on
45 O 1.72143 8.89366 1.31185 3.0 3.0 on
46 O 1.70017 2.78677 1.32608 3.0 3.0 on
47 O 8.80961 9.50685 3.43815 3.0 3.0 on
48 O 8.83087 3.34673 3.42392 3.0 3.0 on
49 Li 0.00693 0.00870 -0.00260 1.5 1.5 on
50 Li -0.00693 6.12480 0.00260 1.5 1.5 on
51 Li 5.24973 0.15951 2.46652 1.5 1.5 on
52 Li 5.28131 5.97399 2.28348 1.5 1.5 on
53 Li 5.26552 9.20025 2.37500 1.5 1.5 on
54 Li 0.00000 3.06675 0.00000 1.5 1.5 on
55 Li 0.00000 9.20025 0.00000 1.5 1.5 on
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors # unit=AU
10.53104666 0. 0.
0. 12.267005455 0.
0. 0. 4.749997002
Atoms.UnitVectors>
# SCF or Electronic System
#
scf.XcType GGA-PBE # GGA-PBE
scf.Hubbard.U on # On|Off , default=off
scf.Hubbard.Occupation dual # onsite|full|dual, default=dual
scf.SpinPolarization on # On|Off
scf.partialCoreCorrection On # On|Off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 370.0 # default=150 (Ry)
#scf.Ngrid 120 70 54
scf.maxIter 80 # default=40
scf.EigenvalueSolver Band # Recursion|Cluster|Band
scf.Kgrid 1 1 2 # means 4x4x4
scf.Mixing.Type Rmm-diis # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.60 # default=0.40
scf.Mixing.History 30 # default=5
scf.Mixing.StartPulay 6 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)
scf.lapack.dste dstegr # dstegr|dstedc|dstevx, default=dstegr
# MD or Geometry Optimization
#
MD.Type NEB # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 7 # default=7
MD.Opt.StartDIIS 30 # default=5
MD.maxIter 150 # default=1
MD.TimeStep 0.5 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)
MD.NEB.Number.Images 8 # default=10
<NEB.Atoms.SpeciesAndCoordinates
1 Mn 2.94895 1.54346 4.62970 10.0 5.0 on
2 Mn 2.96882 7.63908 4.63733 10.0 5.0 on
3 Mn 7.58210 10.72355 0.12030 10.0 5.0 on
4 Mn 7.56222 4.62793 0.11267 10.0 5.0 on
5 Mn 2.32859 10.73363 2.25395 10.0 5.0 on
6 Mn 2.33861 4.60297 2.26942 10.0 5.0 on
7 Mn 8.20246 1.53338 2.49605 10.0 5.0 on
8 Mn 8.19243 7.66404 2.48058 10.0 5.0 on
9 P 0.96264 1.53789 1.96659 2.5 2.5 on
10 P 0.97357 7.66455 1.97641 2.5 2.5 on
11 P 9.56840 10.72911 2.78341 2.5 2.5 on
12 P 9.55748 4.60245 2.77359 2.5 2.5 on
13 P 4.28083 10.74257 4.34742 2.5 2.5 on
14 P 4.26754 4.56194 4.34698 2.5 2.5 on
15 P 6.25022 1.52444 0.40258 2.5 2.5 on
16 P 6.26351 7.70506 0.40302 2.5 2.5 on
17 O 1.00416 1.53546 3.51331 3.0 3.0 on
18 O 1.01898 7.67093 3.52357 3.0 3.0 on
19 O 9.52688 10.73155 1.23668 3.0 3.0 on
20 O 9.51207 4.59608 1.22643 3.0 3.0 on
21 O 4.22011 10.76192 1.14078 3.0 3.0 on
22 O 4.15751 4.45525 1.12646 3.0 3.0 on
23 O 6.31094 1.50509 3.60922 3.0 3.0 on
24 O 6.37354 7.81176 3.62353 3.0 3.0 on
25 O 4.79603 1.52032 0.97379 3.0 3.0 on
26 O 4.80656 7.73005 0.92104 3.0 3.0 on
27 O 5.73502 10.74669 3.77620 3.0 3.0 on
28 O 5.72448 4.53695 3.82895 3.0 3.0 on
29 O 0.48964 10.74666 3.36911 3.0 3.0 on
30 O 0.47523 4.58697 3.36295 3.0 3.0 on
31 O 10.04141 1.52034 1.38089 3.0 3.0 on
32 O 10.05582 7.68003 1.38704 3.0 3.0 on
33 O 8.83098 5.85355 3.42383 3.0 3.0 on
34 O 8.80966 11.96042 3.43810 3.0 3.0 on
35 O 1.70007 6.41346 1.32617 3.0 3.0 on
36 O 1.72138 0.30659 1.31189 3.0 3.0 on
37 O 7.10726 6.49713 0.98321 3.0 3.0 on
38 O 6.99562 0.28588 1.06944 3.0 3.0 on
39 O 3.42379 5.76988 3.76678 3.0 3.0 on
40 O 3.53543 11.98113 3.68056 3.0 3.0 on
41 O 3.53323 9.50120 3.69422 3.0 3.0 on
42 O 3.52774 3.32873 3.61891 3.0 3.0 on
43 O 7.00331 8.93827 1.13108 3.0 3.0 on
44 O 6.99782 2.76581 1.05577 3.0 3.0 on
45 O 1.73404 8.89266 1.31778 3.0 3.0 on
46 O 1.68710 2.78559 1.30679 3.0 3.0 on
47 O 8.84394 9.48142 3.44320 3.0 3.0 on
48 O 8.79701 3.37435 3.43222 3.0 3.0 on
49 Li 0.00000 0.00000 -0.00000 1.5 1.5 on
50 Li -0.00000 6.13350 0.00000 1.5 1.5 on
51 Li 5.26552 -0.00000 2.37500 1.5 1.5 on
52 Li 5.28112 3.22678 2.28325 1.5 1.5 on
53 Li 5.24993 9.04023 2.46675 1.5 1.5 on
54 Li -0.00698 3.07552 0.00262 1.5 1.5 on
55 Li 0.00698 9.19148 -0.00262 1.5 1.5 on
NEB.Atoms.SpeciesAndCoordinates>
scf.restart on
<NEB1.Atoms.SpeciesAndCoordinates
1 Mn 2.96953 1.56110 4.63756 10.0 5.0 on
2 Mn 2.94904 7.65668 4.62937 10.0 5.0 on
3 Mn 7.58201 10.74383 0.12063 10.0 5.0 on
4 Mn 7.56152 4.57240 0.11243 10.0 5.0 on
5 Mn 2.32857 10.73363 2.25411 10.0 5.0 on
6 Mn 2.33892 4.59731 2.26890 10.0 5.0 on
7 Mn 8.19213 1.53620 2.48110 10.0 5.0 on
8 Mn 8.20248 7.66687 2.49589 10.0 5.0 on
9 P 0.97361 1.53572 1.97650 2.5 2.5 on
10 P 0.96267 7.66236 1.96654 2.5 2.5 on
11 P 9.56838 10.73815 2.78346 2.5 2.5 on
12 P 9.55743 4.59778 2.77350 2.5 2.5 on
13 P 4.28083 10.72472 4.34741 2.5 2.5 on
14 P 4.26765 4.63828 4.34691 2.5 2.5 on
15 P 6.26340 1.49522 0.40309 2.5 2.5 on
16 P 6.25022 7.67579 0.40259 2.5 2.5 on
17 O 1.01886 1.52935 3.52368 3.0 3.0 on
18 O 1.00426 7.66475 3.51328 3.0 3.0 on
19 O 9.52678 10.73576 1.23672 3.0 3.0 on
20 O 9.51219 4.60415 1.22632 3.0 3.0 on
21 O 4.22014 10.70545 1.14077 3.0 3.0 on
22 O 4.15748 4.74490 1.12637 3.0 3.0 on
23 O 6.37356 1.38860 3.62363 3.0 3.0 on
24 O 6.31090 7.69506 3.60923 3.0 3.0 on
25 O 4.80637 1.47018 0.92091 3.0 3.0 on
26 O 4.79606 7.67996 0.97392 3.0 3.0 on
27 O 5.73499 10.72055 3.77608 3.0 3.0 on
28 O 5.72467 4.66332 3.82909 3.0 3.0 on
29 O 0.48953 10.72046 3.36923 3.0 3.0 on
30 O 0.47517 4.61336 3.36311 3.0 3.0 on
31 O 10.05588 1.52014 1.38688 3.0 3.0 on
32 O 10.04151 7.68005 1.38077 3.0 3.0 on
33 O 8.79670 5.82602 3.43178 3.0 3.0 on
34 O 8.84402 11.98590 3.44322 3.0 3.0 on
35 O 1.68703 6.41461 1.30678 3.0 3.0 on
36 O 1.73434 0.30748 1.31822 3.0 3.0 on
37 O 6.99772 6.43438 1.05582 3.0 3.0 on
38 O 7.00329 0.26206 1.13110 3.0 3.0 on
39 O 3.52776 5.87145 3.61889 3.0 3.0 on
40 O 3.53333 11.96613 3.69417 3.0 3.0 on
41 O 3.53537 9.48625 3.68049 3.0 3.0 on
42 O 3.42426 3.43022 3.76696 3.0 3.0 on
43 O 6.99567 8.91426 1.06950 3.0 3.0 on
44 O 7.10679 2.70329 0.98304 3.0 3.0 on
45 O 1.72143 8.89366 1.31185 3.0 3.0 on
46 O 1.70017 2.78677 1.32608 3.0 3.0 on
47 O 8.80961 9.50685 3.43815 3.0 3.0 on
48 O 8.83087 3.34673 3.42392 3.0 3.0 on
49 Li 0.00693 0.00870 -0.00260 1.5 1.5 on
50 Li -0.00693 6.12480 0.00260 1.5 1.5 on
51 Li 5.24973 0.15951 2.46652 1.5 1.5 on
52 Li 5.28131 5.668744 2.28348 1.5 1.5 on
53 Li 5.26552 9.20025 2.37500 1.5 1.5 on
54 Li 0.00000 3.06675 0.00000 1.5 1.5 on
55 Li 0.00000 9.20025 0.00000 1.5 1.5 on
NEB1.Atoms.SpeciesAndCoordinates>
.... Plus similar sections for the other images.
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Re: Problem with NEB restart and with specifying path