This thread is locked.Only browsing is available.
Top Page > Browsing
discrepancies results between openmx-siesta-vasp on slab calculation without vdw
Date: 2014/11/12 17:26
Name: Duverger Eric   <eric.duverger@univ-fcomte.fr>

Dear Sir,

in the case of modelisation between a SiC surface and two graphene plane, with siesta or vasp, I obtain a perfect second plane graphene surface decoupled from the first SiC-graphene interface . On the contrary, with openmx, the surface second plane is always deformed and coupled with the SiC-first graphene plane interface.

Please, could you give some informations to obtain the same results.

#
# File Nameori6
#

System.CurrrentDirectory ./ # default=./
DATA.PATH ../open1 # default=../DFT_DATA13
System.Name SiCcomplet
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)


memory.leak on # on|off, default=off

Species.Number 3
<Definition.of.Atomic.Species
H H5.0-s1 H_PBE13
C C5.0-s1p1 C_PBE13
Si Si7.0-s2p2d1 Si_PBE13
Definition.of.Atomic.Species>

Atoms.Number 156
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Si +12.4492516014 +10.9236125147 +2.9786271513 2.0 2.0
2 Si +10.8307694038 +8.1815659084 +3.0184499085 2.0 2.0
3 Si +18.8748443462 +10.9263625959 +2.8602163513 2.0 2.0
4 Si +17.1829752442 +8.0994009514 +2.9395017193 2.0 2.0
5 Si +15.6889642209 +10.8830769547 +2.9588315614 2.0 2.0
6 Si +13.9959746414 +8.0551124737 +3.0340686960 2.0 2.0
7 Si +9.3772183217 +10.9255040216 +2.8152306668 2.0 2.0
8 Si +7.6931372413 +8.2260959610 +2.9722298562 2.0 2.0
9 Si +7.7596557554 +2.6316275943 +3.0170734875 2.0 2.0
10 Si +9.3608414788 +5.3719863601 +3.0114405906 2.0 2.0
11 Si +14.0842343832 +2.6592904676 +2.9052976350 2.0 2.0
12 Si +10.8530224964 +2.6467660187 +2.8837759220 2.0 2.0
13 Si +4.5106161691 +2.6953424602 +3.0013784026 2.0 2.0
14 Si +15.7270871188 +5.4905354110 +2.9279516601 2.0 2.0
15 Si +12.4872507767 +5.3394703594 +2.9766913093 2.0 2.0
16 Si +6.1828124928 +5.5044269746 +3.0254598775 2.0 2.0
17 C +7.7191014775 +0.8087639574 +2.4140560668 2.0 2.0
18 C +12.4295469154 +9.0520910681 +2.4254739856 2.0 2.0
19 C +1.4065637643 +0.8240887929 +2.3654142314 2.0 2.0
20 C +6.0839646062 +9.0696517436 +2.3833931152 2.0 2.0
21 C +10.8955233209 +0.8125460201 +2.3691237071 2.0 2.0
22 C +15.5827568395 +9.0262373219 +2.4103796992 2.0 2.0
23 C +4.5603440590 +0.8718962760 +2.3649143295 2.0 2.0
24 C +9.2876438774 +9.0921243329 +2.3669717550 2.0 2.0
25 C +9.2955615593 +3.5689442470 +2.3727365058 2.0 2.0
26 C +2.9539151717 +3.6179272337 +2.3938988559 2.0 2.0
27 C +12.4599423542 +3.5293590172 +2.3724971712 2.0 2.0
28 C +6.1587082128 +3.6048346167 +2.4565927585 2.0 2.0
29 C +10.9019219565 +6.3133246936 +2.4179775600 2.0 2.0
30 C +4.5932003898 +6.3164650995 +2.3499272157 2.0 2.0
31 C +14.0459127844 +6.2732278465 +2.3783131234 2.0 2.0
32 C +7.7754507635 +6.3569606264 +2.4171983964 2.0 2.0
33 H +7.7381760000 +0.9249120000 +1.2810000000 0.5 0.5
34 H +12.3831760000 +8.9699120000 +1.2810000000 0.5 0.5
35 H +1.5471760000 +0.9249120000 +1.2810000000 0.5 0.5
36 H +6.1921760000 +8.9699120000 +1.2810000000 0.5 0.5
37 H +10.8371760000 +0.9249120000 +1.2810000000 0.5 0.5
38 H +15.4821760000 +8.9699120000 +1.2810000000 0.5 0.5
39 H +4.6391760000 +0.9249120000 +1.2810000000 0.5 0.5
40 H +9.2841760000 +8.9699120000 +1.2810000000 0.5 0.5
41 H +9.2841760000 +3.6069120000 +1.2810000000 0.5 0.5
42 H +3.0931760000 +3.6069120000 +1.2810000000 0.5 0.5
43 H +12.3831760000 +3.6069120000 +1.2810000000 0.5 0.5
44 H +6.1921760000 +3.6069120000 +1.2810000000 0.5 0.5
45 H +10.8371760000 +6.2889120000 +1.2810000000 0.5 0.5
46 H +4.6391760000 +6.2889120000 +1.2810000000 0.5 0.5
47 H +13.9291760000 +6.2889120000 +1.2810000000 0.5 0.5
48 H +7.7381760000 +6.2889120000 +1.2810000000 0.5 0.5
49 C +13.9844818473 +2.5204852702 +4.8623682593 2.0 2.0
50 C +12.5585816531 +0.0272927955 +4.8195853741 2.0 2.0
51 C +1.2718822027 +0.0388136917 +5.1528143411 2.0 2.0
52 C +1.9713744034 +1.2528295837 +5.1633773121 2.0 2.0
53 C +3.3719150406 +1.2549637505 +5.1130677760 2.0 2.0
54 C +4.1105004833 +2.5167017092 +4.9517721569 2.0 2.0
55 C +16.0654797298 +6.1307884417 +4.8314399462 2.0 2.0
56 C +14.7044595987 +3.7590010638 +5.2406159424 2.0 2.0
57 C +3.3441521240 +3.7310280887 +5.3050441700 2.0 2.0
58 C +4.0717235543 +4.9494446342 +5.3255274311 2.0 2.0
59 C +5.4425053423 +4.9180978824 +5.3984509536 2.0 2.0
60 C +6.2001969602 +6.1134095099 +4.9906728638 2.0 2.0
61 C +18.1958363320 +9.8118029010 +5.1957596391 2.0 2.0
62 C +16.7989302959 +7.4559449500 +4.8426439732 2.0 2.0
63 C +5.5004507640 +7.3931772714 +5.1341054114 2.0 2.0
64 C +6.1841196104 +8.5797215381 +5.2435640090 2.0 2.0
65 C +7.6230747478 +8.5746580231 +4.9145592001 2.0 2.0
66 C +8.3316956761 +9.8415621210 +5.1404430606 2.0 2.0
67 C +5.5194344965 +2.4759003394 +5.3905427719 2.0 2.0
68 C +4.0798514242 +0.0330208639 +5.0338079638 2.0 2.0
69 C +5.5601824151 +0.0156356152 +4.9272472458 2.0 2.0
70 C +6.1977598583 +1.2745868209 +5.3740032491 2.0 2.0
71 C +7.6063639910 +1.2617352834 +5.4028927234 2.0 2.0
72 C +8.2514996369 +2.5101665862 +4.9506096199 2.0 2.0
73 C +7.6101535008 +6.1655669844 +5.3910694200 2.0 2.0
74 C +6.1815665030 +3.7114762755 +5.5311785770 2.0 2.0
75 C +7.5898962516 +3.7520568544 +5.4122681942 2.0 2.0
76 C +8.2913482040 +4.9343448390 +5.4067985522 2.0 2.0
77 C +9.7004412181 +4.9881079458 +4.9617050637 2.0 2.0
78 C +10.4432472830 +6.1878336201 +5.4013420243 2.0 2.0
79 C +9.7372558695 +9.8403612786 +5.0869917386 2.0 2.0
80 C +8.3299167310 +7.3481049369 +5.3201338021 2.0 2.0
81 C +9.7273754936 +7.3765346752 +5.3795337265 2.0 2.0
82 C +10.4803461164 +8.5817803848 +4.9834670689 2.0 2.0
83 C +11.8744578313 +8.6380565922 +5.4575973668 2.0 2.0
84 C +12.5743389533 +9.8169077313 +5.4424154226 2.0 2.0
85 C +9.7257588066 +2.4982553655 +5.0672743634 2.0 2.0
86 C +8.2849893880 +0.0681794630 +5.3934094270 2.0 2.0
87 C +9.6862555555 +0.0308537509 +4.9312668733 2.0 2.0
88 C +10.4302486434 +1.2837141902 +5.1331418703 2.0 2.0
89 C +11.8354819457 +1.2897144942 +5.1332418704 2.0 2.0
90 C +12.5361131119 +2.5051165037 +5.1584196691 2.0 2.0
91 C +11.8349927777 +6.2197791331 +5.3375560051 2.0 2.0
92 C +10.4374503683 +3.7216135041 +5.0748757018 2.0 2.0
93 C +11.8398946988 +3.7269479611 +5.1701722159 2.0 2.0
94 C +12.5415606655 +4.9941552654 +4.9350146171 2.0 2.0
95 C +13.9801603174 +4.9931873647 +5.2598859973 2.0 2.0
96 C +14.6547388400 +6.1832830710 +5.1955979412 2.0 2.0
97 C +13.9839762857 +9.8578687917 +5.5293353192 2.0 2.0
98 C +12.5548367276 +7.4090093597 +5.3976788156 2.0 2.0
99 C +13.9720465842 +7.4626818966 +5.0362798583 2.0 2.0
100 C +14.7255404938 +8.6518743694 +5.4608781843 2.0 2.0
101 C +16.0919800465 +8.6238866230 +5.3881994366 2.0 2.0
102 C +16.8213060303 +9.8374158620 +5.2664444275 2.0 2.0
103 C +14.1080471420 +2.5248973469 +8.4451680731 2.0 2.0
104 C +12.6935020440 +0.0775481744 +8.4322139608 2.0 2.0
105 C +1.3765030167 +0.0768585126 +8.4459494354 2.0 2.0
106 C +2.0847516262 +1.3023790996 +8.4552842797 2.0 2.0
107 C +3.4997555600 +1.3028801133 +8.4763151851 2.0 2.0
108 C +4.2061686109 +2.5277504710 +8.4881524558 2.0 2.0
109 C +16.2313476893 +6.2007534449 +8.4699914490 2.0 2.0
110 C +14.8176337180 +3.7528399610 +8.4639705529 2.0 2.0
111 C +3.5004102488 +3.7514835146 +8.4847865092 2.0 2.0
112 C +4.2092044142 +4.9779088735 +8.4846809924 2.0 2.0
113 C +5.6235479297 +4.9759379696 +8.4924395361 2.0 2.0
114 C +6.3299066196 +6.2025165503 +8.4664417908 2.0 2.0
115 C +18.3486690080 +9.8742360081 +8.4412764602 2.0 2.0
116 C +16.9373138008 +7.4248712207 +8.4622795696 2.0 2.0
117 C +5.6211861296 +7.4243226958 +8.4501481789 2.0 2.0
118 C +6.3272359626 +8.6520766354 +8.4397880913 2.0 2.0
119 C +7.7410729375 +8.6531798135 +8.4406445797 2.0 2.0
120 C +8.4483398909 +9.8764216346 +8.4530466516 2.0 2.0
121 C +5.6229255797 +2.5244275879 +8.5123650352 2.0 2.0
122 C +4.2075036881 +0.0779821826 +8.4889352345 2.0 2.0
123 C +5.6186842041 +0.0771791968 +8.5053884777 2.0 2.0
124 C +6.3270237618 +1.3031999151 +8.5129028023 2.0 2.0
125 C +7.7448455263 +1.3012762280 +8.5045612031 2.0 2.0
126 C +8.4520340426 +2.5254127877 +8.5012838554 2.0 2.0
127 C +7.7444862847 +6.2013424873 +8.4683835601 2.0 2.0
128 C +6.3311668853 +3.7523019936 +8.5105874196 2.0 2.0
129 C +7.7459611313 +3.7519636944 +8.5057353805 2.0 2.0
130 C +8.4516638198 +4.9761887521 +8.4828333486 2.0 2.0
131 C +9.8683831849 +4.9765572553 +8.4716563248 2.0 2.0
132 C +10.5739111728 +6.2006108380 +8.4618295024 2.0 2.0
133 C +9.8634261363 +9.8748275990 +8.4736736618 2.0 2.0
134 C +8.4520237610 +7.4266497879 +8.4540962672 2.0 2.0
135 C +9.8636133810 +7.4267253701 +8.4596515784 2.0 2.0
136 C +10.5697216798 +8.6528322916 +8.4728446067 2.0 2.0
137 C +11.9859245830 +8.6540187992 +8.4895423202 2.0 2.0
138 C +12.6900605785 +9.8749429769 +8.5100230829 2.0 2.0
139 C +9.8643239146 +2.5254149210 +8.4770383176 2.0 2.0
140 C +8.4494023693 +0.0768795218 +8.4945630204 2.0 2.0
141 C +9.8642780279 +0.0745994747 +8.4678187797 2.0 2.0
142 C +10.5710369711 +1.3006613678 +8.4575590931 2.0 2.0
143 C +11.9857079409 +1.3011369448 +8.4410438862 2.0 2.0
144 C +12.6935221690 +2.5255259804 +8.4430429656 2.0 2.0
145 C +11.9870831510 +6.2010740496 +8.4562056018 2.0 2.0
146 C +10.5734920180 +3.7524124316 +8.4696509664 2.0 2.0
147 C +11.9872566234 +3.7503723576 +8.4530190296 2.0 2.0
148 C +12.6958122902 +4.9749535671 +8.4485218355 2.0 2.0
149 C +14.1099469576 +4.9756257036 +8.4578373087 2.0 2.0
150 C +14.8157129534 +6.2018572537 +8.4577322606 2.0 2.0
151 C +14.1068268568 +9.8742112554 +8.5039906440 2.0 2.0
152 C +12.6944253167 +7.4262524993 +8.4678084883 2.0 2.0
153 C +14.1074673172 +7.4246889109 +8.4688507141 2.0 2.0
154 C +14.8141299761 +8.6513057316 +8.4915513396 2.0 2.0
155 C +16.2276483895 +8.6495831585 +8.4704790083 2.0 2.0
156 C +16.9355752346 +9.8748377999 +8.4633586534 2.0 2.0
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
12.7300000000000004 0.0000000000000000 0.0000000000000000
6.3650000000000002 11.0245033901999996 0.0000000000000000
0.0000000000000000 0.0000000000000000 40.0000000000000000
Atoms.UnitVectors>


<MD.Fixed.XYZ
1 0 0 0
2 0 0 0
3 0 0 0
4 0 0 0
5 0 0 0
6 0 0 0
7 0 0 0
8 0 0 0
9 0 0 0
10 0 0 0
11 0 0 0
12 0 0 0
13 0 0 0
14 0 0 0
15 0 0 0
16 0 0 0
17 0 0 0
18 0 0 0
19 0 0 0
20 0 0 0
21 0 0 0
22 0 0 0
23 0 0 0
24 0 0 0
25 0 0 0
26 0 0 0
27 0 0 0
28 0 0 0
29 0 0 0
30 0 0 0
31 0 0 0
32 0 0 0
33 1 1 1
34 1 1 1
35 1 1 1
36 1 1 1
37 1 1 1
38 1 1 1
39 1 1 1
40 1 1 1
41 1 1 1
42 1 1 1
43 1 1 1
44 1 1 1
45 1 1 1
46 1 1 1
47 1 1 1
48 1 1 1
49 0 0 0
50 0 0 0
51 0 0 0
52 0 0 0
53 0 0 0
54 0 0 0
55 0 0 0
56 0 0 0
57 0 0 0
58 0 0 0
59 0 0 0
60 0 0 0
61 0 0 0
62 0 0 0
63 0 0 0
64 0 0 0
65 0 0 0
66 0 0 0
67 0 0 0
68 0 0 0
69 0 0 0
70 0 0 0
71 0 0 0
72 0 0 0
73 0 0 0
74 0 0 0
75 0 0 0
76 0 0 0
77 0 0 0
78 0 0 0
79 0 0 0
80 0 0 0
81 0 0 0
82 0 0 0
83 0 0 0
84 0 0 0
85 0 0 0
86 0 0 0
87 0 0 0
88 0 0 0
89 0 0 0
90 0 0 0
91 0 0 0
92 0 0 0
93 0 0 0
94 0 0 0
95 0 0 0
96 0 0 0
97 0 0 0
98 0 0 0
99 0 0 0
100 0 0 0
101 0 0 0
102 0 0 0
103 0 0 0
104 0 0 0
105 0 0 0
106 0 0 0
107 0 0 0
108 0 0 0
109 0 0 0
110 0 0 0
111 0 0 0
112 0 0 0
113 0 0 0
114 0 0 0
115 0 0 0
116 0 0 0
117 0 0 0
118 0 0 0
119 0 0 0
120 0 0 0
121 0 0 0
122 0 0 0
123 0 0 0
124 0 0 0
125 0 0 0
126 0 0 0
127 0 0 0
128 0 0 0
129 0 0 0
130 0 0 0
131 0 0 0
132 0 0 0
133 0 0 0
134 0 0 0
135 0 0 0
136 0 0 0
137 0 0 0
138 0 0 0
139 0 0 0
140 0 0 0
141 0 0 0
142 0 0 0
143 0 0 0
144 0 0 0
145 0 0 0
146 0 0 0
147 0 0 0
148 0 0 0
149 0 0 0
150 0 0 0
151 0 0 0
152 0 0 0
153 0 0 0
154 0 0 0
155 0 0 0
156 0 0 0
MD.Fixed.XYZ>

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 300.0 # default=150 (Ry)
scf.maxIter 60 # default=40
scf.EigenvalueSolver cluster # DC|Cluster|Band krylov
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 0.010 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.100 # default=0.40

scf.Kerker.factor 30.0

scf.Mixing.History 30 # default=5
scf.Mixing.StartPulay 15 # default=6


MD.Type EF # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 30 # default=5
MD.Opt.EveryDIIS 200 # default=10
MD.maxIter 900 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 0.001 # default=1.0e-4 (Hartree/bohr)

メンテ
Page: [1]

Re: discrepancies results between openmx-siesta-vasp on slab calculation without vdw ( No.1 )
Date: 2014/11/13 09:21
Name: T. Ozaki

Hi,

I also performed similar calculations with different basis sets and obtained optimized
structures as shown at http://www.openmx-square.org/forum/img/SiC-Gra.pdf
The case (A) with your specification for the basis set leads to the modulation of
the second graphene, while the case (B) with a rich basis set gives us the nearly planar
structure of the second graphene.

Since C5.0-s1p1 is regarded as a poor basis set for carbon, the bond length between C-C
is overestimated. Under the fixed lattice constant, the graphene sheet tries to buckle
to keep the overestimated bond length. This is the reason why the second layer is modulated.
On the other hand, the rich basis set gives a nearly convergent bond length, leading to
the planar structure of the second graphene layer.

Regards,

TO
メンテ
Re: discrepancies results between openmx-siesta-vasp on slab calculation without vdw ( No.2 )
Date: 2014/11/14 06:30
Name: Duverger  <eric.duverger@univ-fcomte.fr>

Thank you very much for your response.

Regards

ED

メンテ

Page: [1]