# [DFTB-Plus-User] DFTB-MD with surfaces and amorphous materials

Vanessa Gruner vgruner08 at gmail.com
Thu Jun 20 19:03:40 CEST 2013

```Dear DFTB+ Community,

I have a couple of very general newbie questions:

(1) Can DFTB+ be used to perform MD simulations with surfaces? I gather
from one of the example MD simulations, 'SiH-surface', that comes with the
with surfaces. However, when I tried a simple test, in which I took the
input from a well-behaved DFTB-MD simulation and increased the lattice
vector along the z-axis (to reflect a surface), I found that the first time
step of the simulation doesn't converge. (See input below. I'm using
version 1.2.2.) Am I correct about my assumption that DFTB+ can perform
DFTB-MD simulations with surfaces? If so, what might I be doing incorrectly?

(2) My other somewhat related question is about whether or not DFTB+ is
appropriate to perform DFTB-MD simulations with amorphous systems. I assume
that this is true if the system is treated as a non-periodic (or "cluster")
system, but is it possible to treat them as a periodic system?

Vanessa

*****************************************
Geometry = GenFormat {
72  S
Si  O
1  1    2.72029188          0.02565985          3.56986498
2  1   -1.37222083          2.37392581          7.18904764
3  1    3.55772121          6.24406872          5.34132995
4  1    2.73015909          0.02472705          9.02003048
5  1    3.50916011          6.19491278          0.05278952
6  1   -1.36587576          2.33303499          1.82845551
7  1    0.21392498          4.22011286          3.61758699
8  1    1.15483394          6.52817653          7.15472754
9  1   -1.36623812          6.16013967          5.41390632
10  1    3.54494407          2.34389853          7.24386288
11  1    5.12837336          4.32361900          8.99186871
12  1    5.98616310          1.91961151          0.03495400
13  1    0.21520582          4.25139273          9.03527082
14  1    1.06553066          6.50331471          1.80351714
15  1   -1.39473082          6.17984802          0.01011540
16  1    3.53020826          2.29806647          1.78274061
17  1    5.15076019          4.23935875          3.55101978
18  1    6.09586279          1.94097506          5.39601692
19  1    7.59562220         -0.01773099          3.63060204
20  1   -3.82008684          6.61140748          7.18137783
21  1    1.16335163          1.92884348          5.26701562
22  1    7.62369313          0.01700696          8.99464123
23  1    1.06938209          1.94121886          0.05176643
24  1   -3.82202230          6.58354265          1.85185380
25  2    1.40523314          2.95988133          3.91037753
26  2    1.72708303          8.16566341          7.56525561
27  2   -3.09201949          5.85154799          5.73260807
28  2    1.88040125          2.51381062          6.77289690
29  2    6.20118782          5.70060814          8.67816575
30  2    6.67777601          0.31785142         10.47693632
31  2    1.37849458          3.01733602          9.52912724
32  2    1.71745110          8.15969498          2.22027835
33  2   -3.02369228          5.89872596          0.47635861
34  2    1.87931034          2.73459028          1.42254714
35  2    6.33071833          5.48571989          3.15008045
36  2    6.62798744          0.27547538          5.06637954
37  2   -1.15745896          7.15714647          3.96139812
38  2   -0.72352703          3.96347390          7.59500119
39  2    1.86999733          5.86446794          5.70552614
40  2    6.74210430          2.63808881          6.88031381
41  2    3.81759200          1.32336620          8.60788019
42  2    4.24131553          4.64083334         10.49970063
43  2   -1.08919738          7.18892320          9.40124848
44  2   -0.75250995          3.96097559          2.18066948
45  2    1.83532070          5.79569727          0.42871622
46  2    6.73504120          2.64448581          1.45530780
47  2    3.84161978          1.31181380          3.21820223
48  2    4.12056514          4.61741162          4.92551810
49  2    6.26774240          2.89059882          3.93983572
50  2    4.15063155          3.96650498          7.60839534
51  2    4.40995040          1.78801055          5.83118613
52  2   -0.57727847          6.86055182          6.82264507
53  2    1.39430503          5.52661016          8.59877109
54  2   -0.74451401          4.58449606         10.45304285
55  2    6.23477664          2.94319410          9.42351343
56  2    4.12147464          3.94439978          2.16924673
57  2    4.26871693          1.58645338          0.35604353
58  2   -0.61279677          6.81115334          1.44357649
59  2    1.32523790          5.52790682          3.22924026
60  2   -0.63346226          4.55474534          5.11798764
61  2    3.80091615          7.19353005          3.90780547
62  2   -3.20794979          8.21850114          7.58724208
63  2   -0.48512069          1.58266627          5.85414470
64  2    4.29795902          6.89007052          6.79014187
65  2    8.75619117          1.33174219          8.55370307
66  2    1.67319916          0.36795164         10.37735539
67  2    3.75094225          7.17047171          9.40095731
68  2   -3.19744949          8.18000919          2.19540628
69  2   -0.59341297          1.59403384          0.43541051
70  2    4.35867928          6.93475162          1.39258447
71  2    8.68551580          1.38259432          3.28564629
72  2    1.77900077          0.29799634          4.98907353
0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
0.9831999779E+01    0.0000000000E+00    0.0000000000E+00
-0.4915999889E+01    0.8514761578E+01    0.0000000000E+00
0.0000000000E+00    0.0000000000E+00    0.3081079960E+02
}

Driver = VelocityVerlet {
MovedAtoms    = 1:-1
Velocities [AA/ps] = {
1.22753846     -1.44549148      0.52007986
-1.16193226      1.71592427     -2.96611350
-0.51667226      1.31320209     -2.78464533
0.82387823      0.33802238     -2.21187591
-2.51680060      0.66617915     -0.61438977
-3.45626295      2.28719719      0.29441515
1.07307343     -0.07288983     -2.30689875
2.22366769     -1.97910220     -1.05908445
-0.95882292     -1.52778550      0.32084103
-1.77628300      1.58857242      3.24715008
0.88382664      1.47243976      4.68113718
-2.07937571     -1.23264950      0.57036683
4.14406529      0.15671592      1.50681738
0.44051811     -2.25148849      3.86903633
1.54368782      1.26653496     -2.42653728
-1.07582066      2.32594260     -2.12237650
-0.39890523     -0.83498218     -2.74967070
2.39615353     -0.48038060      2.82249789
1.72259485      0.73730937      2.04515594
-1.59796575      3.78745593     -2.25883529
1.51940242     -1.41547387     -1.29902560
0.98467632      1.07344599     -0.07328004
-0.73787674      0.80889372      6.39192641
-3.51863797     -3.26170432      2.04789623
4.09303429      0.45320776     -5.37189146
0.86974831     -1.55123708     -0.49924088
0.22152156     -0.81668737      0.43382563
0.00763047     -3.05030672     -2.33657206
-2.42572519      3.16593102      1.99941078
3.71843851      0.97053809     -0.87313943
0.72487903     12.03699397     -2.37832765
-4.82622604     -6.00211298     -3.72686610
-3.39989204     -3.41048293      0.13057839
-1.79667030      0.80258189     -2.40023694
3.59186973     -5.16805783     -1.99675412
-0.44235455      1.97935774      2.08463153
-0.72773016     -2.62383138      0.17179600
0.40127289      3.36656663     -0.40458922
-0.83668930     -0.33097833     -2.09003112
2.62994405     -0.49309820     -1.63218759
3.60643570      1.23299920     -0.11822295
6.51102023     -0.52328831     -2.08384835
-1.09047170     -2.03615938      6.24703162
-0.71906732     -1.50425636      1.41861427
-1.26788200     -4.81906584      0.49266156
2.03538659      0.34059597      2.72112477
2.06492685     -0.97953432     -0.89816048
-0.35600170      0.19177333     -5.15641654
0.98213957     -0.45888567     -2.76585232
-3.09374997      3.53340146     -1.00631856
3.72491724      2.46156787     -5.95468074
-1.29928529     -2.42910114     -3.08752557
-0.62200328     -4.94293908     -3.00594796
-1.95500872      0.15902263      2.06576833
-3.39441759      5.12135052      0.45093699
-1.04421151     -3.34798669      0.93375210
-3.65841706     -2.13278069      1.40192497
-4.15365092     -0.65839278      1.48891675
-1.80647764     -0.94435141     -2.38003704
1.20714017      1.22122294      7.55162096
1.89954630      0.71674953     -3.15041137
1.29633496     -1.58329089      1.53311070
1.16545631     -1.60534347      1.92635599
0.08063520      0.23817491     -1.91089349
0.63677512     -3.99598599      1.49466883
-1.42568040     -2.02168443      0.22120892
-2.82862914     -1.57720374      2.92832762
3.25406746      9.38256937      2.28477207
-4.05067766     -2.44675467      4.28279371
2.37947502      5.61599558      3.02005787
-2.75312466     -0.01223718      4.31250136
4.29640214     -0.35891559     -5.91956245
}
Steps = 2000
TimeStep [fs] = 0.1
Thermostat = None {}
MDRestartFrequency = 100
OutputPrefix       = "quartz_md"
}

Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1e-5
OrbitalResolvedSCC = No
OldSKInterpolation = No
MaxSCCIterations = 10000
Mixer = Broyden {
MixingParameter = 0.200000000000000
CachedIterations = -1
InverseJacobiWeight = 1.000000000000000E-002
MinimalWeight = 1.00000000000000
MaximalWeight = 100000.000000000
WeightFactor = 1.000000000000000E-002
}
MaxAngularMomentum = {
Si = d
O = p
}
SlaterKosterFiles {
Si-Si = "Si-Si.skf"
Si-O = "Si-O.skf"
O-Si = "Si-O.skf"
O-O = "O-O.skf"
}
ElectricField = {}
DampXH = No
Charge = 0.000000000000000E+000
InitialCharges = {
AllAtomCharges = { # Speci.es net charge for each atom in an H2O
molecule
1.30958331
1.31119409
1.31679545
1.32863581
1.33291809
1.30459996
1.31828382
1.30551616
1.29758822
1.35624475
1.30784758
1.29873300
1.31695328
1.31888638
1.32985898
1.30287569
1.31391109
1.31513485
1.30830689
1.30065070
1.32773165
1.30290642
1.32640109
1.35898748
-0.63813262
-0.65882998
-0.66209268
-0.66906995
-0.65133031
-0.66310043
-0.65830731
-0.67956518
-0.65804428
-0.65235738
-0.65132304
-0.65242555
-0.66837687
-0.65721619
-0.63720581
-0.64472522
-0.64505705
-0.65941631
-0.66216887
-0.64769151
-0.63858459
-0.64977274
-0.64962679
-0.66675013
-0.65960218
-0.65731063
-0.68712602
-0.65675302
-0.66156443
-0.66398658
-0.67638893
-0.65178648
-0.65532433
-0.65790934
-0.64984980
-0.66303605
-0.64784234
-0.65446820
-0.68820843
-0.65316206
-0.65413740
-0.66886040
-0.65450020
-0.68146765
-0.64679716
-0.66728486
-0.67983474
-0.65217272
}
}
SpinConstants = {
Si = {
# Wss Wsp Wsd Wps Wpp Wpd Wds Wdp  Wdd
-0.002 -0.015 0.02 -0.015 -0.014 0.002 0.00 0.00 -0.032
}
O = {
# Wss Wsp Wps Wpp
-0.035 -0.030 -0.030 -0.028
}
}
SpinPolarisation = Colinear {
UnpairedElectrons = 0.0
InitialSpins = {}
}
Eigensolver = DivideAndConquer {}
Filling = Fermi {
Temperature [Kelvin] = 1.0
}
KPointsAndWeights = {
0.0 0.0 0.0 1.0
}
OrbitalPotential = {}
Dispersion = {}
}

Options {
WriteAutotestTag = Yes
WriteEigenvectors = Yes
WriteDetailedXML = No
WriteResultsTag = No
WriteDetailedOut = Yes
WriteBandOut = Yes
AtomResolvedEnergies = No
RandomSeed = 0
MinimiseMemoryUsage = No
}

ParserOptions {
ParserVersion = 4
WriteHSDInput = Yes
WriteXMLInput = No
StopAfterParsing = No
IgnoreUnprocessedNodes = No
}
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20130620/d1acfbfe/attachment-0001.html>
```