nan error in optimization of Fe doped Arm chair graphene nano ribbon

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nan error in optimization of Fe doped Arm chair graphene nano ribbon

Date: 2019/08/20 21:57
Name: Lovleen Kaur <lovleenkaurkkr@gmail.com>: Dear Developers
I am optimizing AGNR(arm chair graphene nano ribbon) with Fe doping. I want to study Vander walls interactions so i am using DFT D3 calculations using BJ damping but the calculation stops after one step giving value NAN in total energy.I have applied patch that you have provided to correct this error till the problem continues. Please suggest
Here is the input file

System.CurrrentDirectory ./
System.Name graphene
DATA.PATH ../../../../../../DFT_DATA13
level.of.stdout 1
level.of.fileout 1

Species.Number 3
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE13
C C6.0-s2p2d1 C_PBE13
Fe Fe8.0S-s2p2d1 Fe_PBE13S
Definition.of.Atomic.Species>

Atoms.Number 110
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 C 0.7530863 1.2579184 -0.0021737 2.00000 2.00000
2 C 2.1285052 1.2579184 -0.0021737 2.00000 2.00000
3 C 5.0557442 1.2579185 -0.0021737 2.00000 2.00000
4 C 9.3584024 1.2579185 -0.0021737 2.00000 2.00000
5 C 6.4311631 1.2579183 -0.0021737 2.00000 2.00000
6 C 10.7338208 1.2579185 -0.0021737 2.00000 2.00000
7 C 0.0123332 2.4621175 -0.0021737 2.00000 2.00000
8 C 0.0040635 4.9346071 -0.0021737 2.00000 2.00000
9 C 0.0040635 7.3958628 -0.0021737 2.00000 2.00000
10 C 0.0123333 9.8683525 -0.0021737 2.00000 2.00000
11 C 2.8692583 2.4621175 -0.0021737 2.00000 2.00000
12 C 2.8775280 4.9346071 -0.0021737 2.00000 2.00000
13 C 2.8775280 7.3958629 -0.0021737 2.00000 2.00000
14 C 2.8692582 9.8683526 -0.0021737 2.00000 2.00000
15 C 0.7240061 3.6937611 -0.0021737 2.00000 2.00000
16 C 0.7206887 6.1652351 -0.0021737 2.00000 2.00000
17 C 0.7240061 8.6367090 -0.0021737 2.00000 2.00000
18 C 0.7530860 11.0725517 -0.0021737 2.00000 2.00000
19 C 2.1575854 3.6937611 -0.0021737 2.00000 2.00000
20 C 2.1609028 6.1652351 -0.0021737 2.00000 2.00000
21 C 2.1575854 8.6367089 -0.0021737 2.00000 2.00000
22 C 2.1285055 11.0725516 -0.0021737 2.00000 2.00000
23 C 4.3149912 2.4621174 -0.0021737 2.00000 2.00000
24 C 4.3067215 4.9346072 -0.0021737 2.00000 2.00000
25 C 4.3067214 7.3958630 -0.0021737 2.00000 2.00000
26 C 4.3149911 9.8683526 -0.0021737 2.00000 2.00000
27 C 8.6176490 2.4621175 -0.0021737 2.00000 2.00000
28 C 8.6093793 4.9346071 -0.0021737 2.00000 2.00000
29 C 8.6093793 7.3958630 -0.0021737 2.00000 2.00000
30 C 8.6176490 9.8683526 -0.0021737 2.00000 2.00000
31 C 7.1719163 2.4621175 -0.0021737 2.00000 2.00000
32 C 7.1801859 4.9346071 -0.0021737 2.00000 2.00000
33 C 7.1801860 7.3958629 -0.0021737 2.00000 2.00000
34 C 7.1719163 9.8683525 -0.0021737 2.00000 2.00000
35 C 11.4745742 2.4621174 -0.0021737 2.00000 2.00000
36 C 11.4828438 4.9346072 -0.0021737 2.00000 2.00000
37 Fe 11.4828438 7.3958629 -0.0021737 8.00000 6.00000
38 C 11.4745742 9.8683526 -0.0021737 2.00000 2.00000
39 C 5.0266641 3.6937612 -0.0021737 2.00000 2.00000
40 C 5.0233466 6.1652350 -0.0021737 2.00000 2.00000
41 C 5.0266641 8.6367088 -0.0021737 2.00000 2.00000
42 C 5.0557444 11.0725516 -0.0021737 2.00000 2.00000
43 C 9.3293221 3.6937612 -0.0021737 2.00000 2.00000
44 C 9.3260046 6.1652350 -0.0021737 2.00000 2.00000
45 C 9.3293221 8.6367089 -0.0021737 2.00000 2.00000
46 C 9.3584026 11.0725516 -0.0021737 2.00000 2.00000
47 C 6.4602433 3.6937611 -0.0021737 2.00000 2.00000
48 C 6.4635608 6.1652350 -0.0021737 2.00000 2.00000
49 C 6.4602432 8.6367089 -0.0021737 2.00000 2.00000
50 C 6.4311630 11.0725517 -0.0021737 2.00000 2.00000
51 C 10.7629011 3.6937612 -0.0021737 2.00000 2.00000
52 C 10.7662187 6.1652350 -0.0021737 2.00000 2.00000
53 C 10.7629012 8.6367089 -0.0021737 2.00000 2.00000
54 C 10.7338207 11.0725516 -0.0021737 2.00000 2.00000
55 H 0.2371719 0.2998919 -0.0021737 0.50000 0.50000
56 H 2.6444196 0.2998919 -0.0021737 0.50000 0.50000
57 H 4.5398298 0.2998919 -0.0021737 0.50000 0.50000
58 H 6.9470775 0.2998919 -0.0021737 0.50000 0.50000
59 H 8.8424877 0.2998919 -0.0021737 0.50000 0.50000
60 H 11.2497355 0.2998919 -0.0021737 0.50000 0.50000
61 H 11.2497355 12.0305782 -0.0021737 0.50000 0.50000
62 H 8.8424877 12.0305782 -0.0021737 0.50000 0.50000
63 H 6.9470776 12.0305781 -0.0021737 0.50000 0.50000
64 H 4.5398298 12.0305782 -0.0021737 0.50000 0.50000
65 H 2.6444195 12.0305781 -0.0021737 0.50000 0.50000
66 H 0.2371720 12.0305781 -0.0021737 0.50000 0.50000
67 C 13.6610602 1.2579184 -0.0021737 2.00000 2.00000
68 C 15.0364788 1.2579185 -0.0021737 2.00000 2.00000
69 C 17.9637181 1.2579184 -0.0021737 2.00000 2.00000
70 C 19.3391368 1.2579184 -0.0021737 2.00000 2.00000
71 C 12.9203070 2.4621175 -0.0021737 2.00000 2.00000
72 C 12.9120373 4.9346071 -0.0021737 2.00000 2.00000
73 C 12.9120373 7.3958628 -0.0021737 2.00000 2.00000
74 C 12.9203071 9.8683525 -0.0021737 2.00000 2.00000
75 C 15.7772321 2.4621174 -0.0021737 2.00000 2.00000
76 C 15.7855018 4.9346071 -0.0021737 2.00000 2.00000
77 C 15.7855017 7.3958630 -0.0021737 2.00000 2.00000
78 C 15.7772320 9.8683526 -0.0021737 2.00000 2.00000
79 C 13.6319800 3.6937611 -0.0021737 2.00000 2.00000
80 C 13.6286625 6.1652351 -0.0021737 2.00000 2.00000
81 C 13.6319798 8.6367090 -0.0021737 2.00000 2.00000
82 C 13.6610600 11.0725517 -0.0021737 2.00000 2.00000
83 C 15.0655591 3.6937612 -0.0021737 2.00000 2.00000
84 C 15.0688766 6.1652350 -0.0021737 2.00000 2.00000
85 C 15.0655592 8.6367089 -0.0021737 2.00000 2.00000
86 C 15.0364791 11.0725516 -0.0021737 2.00000 2.00000
87 C 17.2229649 2.4621175 -0.0021737 2.00000 2.00000
88 C 17.2146952 4.9346072 -0.0021737 2.00000 2.00000
89 C 17.2146952 7.3958629 -0.0021737 2.00000 2.00000
90 C 17.2229649 9.8683525 -0.0021737 2.00000 2.00000
91 C 20.0798900 2.4621175 -0.0021737 2.00000 2.00000
92 C 20.0881597 4.9346072 -0.0021737 2.00000 2.00000
93 C 20.0881597 7.3958630 -0.0021737 2.00000 2.00000
94 C 20.0798900 9.8683527 -0.0021737 2.00000 2.00000
95 C 17.9346379 3.6937611 -0.0021737 2.00000 2.00000
96 C 17.9313204 6.1652350 -0.0021737 2.00000 2.00000
97 C 17.9346379 8.6367090 -0.0021737 2.00000 2.00000
98 C 17.9637184 11.0725517 -0.0021737 2.00000 2.00000
99 C 19.3682171 3.6937612 -0.0021737 2.00000 2.00000
100 C 19.3715346 6.1652350 -0.0021737 2.00000 2.00000
101 C 19.3682170 8.6367088 -0.0021737 2.00000 2.00000
102 C 19.3391365 11.0725515 -0.0021737 2.00000 2.00000
103 H 13.1451457 0.2998919 -0.0021737 0.50000 0.50000
104 H 15.5523934 0.2998919 -0.0021737 0.50000 0.50000
105 H 17.4478036 0.2998919 -0.0021737 0.50000 0.50000
106 H 19.8550513 0.2998919 -0.0021737 0.50000 0.50000
107 H 19.8550513 12.0305782 -0.0021737 0.50000 0.50000
108 H 17.4478036 12.0305782 -0.0021737 0.50000 0.50000
109 H 15.5523934 12.0305781 -0.0021737 0.50000 0.50000
110 H 13.1451457 12.0305781 -0.0021737 0.50000 0.50000
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
21.51329 0.00000 -0.00000
0.00000 30.03302 0.00000
-0.00000 0.00000 29.99564
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization on
scf.ElectronicTemperature 300.0
scf.energycutoff 250.0
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 5 1 1
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7

#
# vdW
#

scf.dftD on
version.dftD 3
DFTD3.damp bj
DFTD.IntDirection 0 0 0
DFT.scale6 1.0
DFT.scale8 0.7875
DFTD.a1 0.4289
DFT.a2 4.4407

#
# MD or Geometry Optimization
#

MD.Type RF # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 30 # default=5
#MD.Opt.EveryDIIS 10000 # default=10
MD.maxIter 500 #
MD.Opt.criterion 2.0e-4 # default=1.0e-4 (a.u.)

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Re: nan error in optimization of Fe doped Arm chair graphene nano ribbon ( No.1 )

Date: 2019/09/19 11:02
Name: Jhon W. Gonzalez

Hi,

There is a bug in the calculation of the energy with the D3 van der Waals correction, and it seems like the latest patch fixes it.
With the previous patch, for DFTD3.damp = bj I get UvdW = -nan and for DFTD3.damp = zero I get UvdW = 0.000.

I just used the D2 correction.

Best,

Jhon W.

Page: [1]