[DFTB-Plus-User] MD simulation get stuck without errors
Xiuyuan Li
18801188299 at 163.com
Tue Aug 18 11:09:15 CEST 2020
Hello, everyone
I performed Molecular Dynamics by DFTB+ and something happened as this page mentioned,
(https://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/2019/002987.html)
but there is no final solution in that page.
Every MD simulation got stuck after different number MD steps, the jobs were running, but no new optput documents.
It seems not a common problem, since I can find little advice in Google.
Please help me,
thanks.
Lee
My input is as follows:
Geometry = GenFormat {
<<< geo.gen
}
Driver = VelocityVerlet {
TimeStep [Femtosecond] = 1
Thermostat = NoseHoover {
CouplingStrength [cm^-1] = 3000
Temperature [Kelvin] = TemperatureProfile {
constant 1 300
linear 45000 3000
}
AdaptFillingTemp = Yes
}
MDRestartFrequency = 3
}
Hamiltonian = DFTB {
SCC = Yes
ThirdOrderFull = Yes
MaxAngularMomentum {
C = "p"
N = "p"
H = "s"
O = "p"
}
SlaterKosterFiles = Type2FileNames {
Prefix = "/home-yw/users/nsyw1284/lxy/DFTB+/3ob-3-1/"
Separator = "-"
Suffix = ".skf"
}
KPointsAndWeights = {
0 0 0 1
}
HCorrection = Damping {
Exponent = 4.05
}
HubbardDerivs = {
C = -0.1492
N = -0.1535
H = -0.1857
O = -0.1575
}
Dispersion = DftD3 {
Damping = BeckeJohnson {
a1 = 0.746
a2 = 4.191
}
s6 = 1.0
s8 = 3.209
}
}
Analysis = {
MullikenAnalysis = No
WriteBandOut = No
}
Parallel {
UseOmpThreads = Yes
}
And this is geo.gen:
304 S
C H N O
1 1 0.8616664105E+01 0.2820077206E+01 0.3667859383E+00
2 1 0.8078931888E+01 0.3620333664E+01 0.1410428657E+01
3 1 0.6870067234E+01 0.3301697072E+01 0.2054126474E+01
4 1 0.6200656706E+01 0.2132819008E+01 0.1681430020E+01
5 1 0.6695032792E+01 0.1314065716E+01 0.6626639013E+00
6 1 0.7875523094E+01 0.1673685362E+01 0.2923820015E-02
7 1 0.4407648617E+01 0.3133719544E+01 0.1273863102E+02
8 1 0.1004624723E+01 0.2887363133E+01 0.1626341419E+01
9 1 0.1811922091E+01 0.4045796770E+01 0.1683930730E+01
10 1 0.2206722603E+01 0.4607462591E+01 0.2899175084E+01
11 1 0.1855291256E+01 0.3969392671E+01 0.4094150443E+01
12 1 0.1104222562E+01 0.2783262780E+01 0.4091497649E+01
13 1 0.6665215493E+00 0.2272427544E+01 0.2858311121E+01
14 1 0.4767857935E+00 0.2425381744E+01 0.3208931446E+00
15 1 0.9558954009E+01 0.4517301169E-01 0.5737948637E+01
16 1 0.1009664887E+02 0.8454492917E+00 0.4694307357E+01
17 1 0.1130549975E+02 0.5268516784E+00 0.4050570613E+01
18 1 0.1197489770E+02 0.1045741858E+02 0.4423299227E+01
19 1 0.1148055614E+02 0.9638637476E+01 0.5442060271E+01
20 1 0.1030006515E+02 0.9998211560E+01 0.6101824162E+01
21 1 0.8273678186E+01 0.3587423610E+00 0.6416533334E+01
22 1 0.1717096798E+02 0.1124318007E+00 0.4478314269E+01
23 1 0.1636366880E+02 0.1270861992E+01 0.4420725469E+01
24 1 0.1596886162E+02 0.1832514555E+01 0.3205480326E+01
25 1 0.1632028478E+02 0.1194429852E+01 0.2010507000E+01
26 1 0.1707130190E+02 0.1110773032E+02 0.2013220926E+01
27 1 0.1750901518E+02 0.1059691360E+02 0.3246411821E+01
28 1 0.1769878623E+02 0.1074991836E+02 0.5783823186E+01
29 1 0.6811765792E+01 0.2729675620E+01 0.1226307400E+02
30 1 0.7349497943E+01 0.1929419119E+01 0.1121943132E+02
31 1 0.8558362571E+01 0.2248055608E+01 0.1057573346E+02
32 1 0.9227773113E+01 0.3416933677E+01 0.1094842984E+02
33 1 0.8733397081E+01 0.4235687019E+01 0.1196719592E+02
34 1 0.7552906806E+01 0.3876067433E+01 0.1262693605E+02
35 1 0.1102078128E+02 0.2416033369E+01 -0.1087711056E+00
36 1 0.1442380499E+02 0.2662389588E+01 0.1100351874E+02
37 1 0.1361650761E+02 0.1503955932E+01 0.1094592942E+02
38 1 0.1322170699E+02 0.9422901240E+00 0.9730685068E+01
39 1 0.1357313823E+02 0.1580360141E+01 0.8535709726E+01
40 1 0.1432420697E+02 0.2766489966E+01 0.8538362549E+01
41 1 0.1476190818E+02 0.3277325119E+01 0.9771549026E+01
42 1 0.1495164395E+02 0.3124371022E+01 0.1230896699E+02
43 1 0.5869449082E+01 0.1105429318E+02 0.6891943290E+01
44 1 0.5331754360E+01 0.1025401676E+02 0.7935584489E+01
45 1 0.4122903506E+01 0.1057261414E+02 0.8579321339E+01
46 1 0.3453505548E+01 0.6420473019E+00 0.8206592951E+01
47 1 0.3947846979E+01 0.1460828584E+01 0.7187831990E+01
48 1 0.5128337861E+01 0.1101254579E+01 0.6528067875E+01
49 1 0.7154724917E+01 0.1074072396E+02 0.6213358607E+01
50 1 -0.1742564678E+01 0.1098703417E+02 0.8151577424E+01
51 1 -0.9352655462E+00 0.9828603915E+01 0.8209166256E+01
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53 1 -0.8918813480E+00 0.9905036166E+01 0.1061938470E+02
54 1 -0.1642898426E+01 -0.8264319358E-02 0.1061667073E+02
55 1 -0.2080611842E+01 0.5025523449E+00 0.9383479877E+01
56 1 -0.2270382948E+01 0.3495476540E+00 0.6846068528E+01
57 1 0.8616637936E+01 0.8369790512E+01 0.3668180782E+00
58 1 0.8078905722E+01 0.9170046954E+01 0.1410460798E+01
59 1 0.6870041014E+01 0.8851410402E+01 0.2054158529E+01
60 1 0.6200630481E+01 0.7682532347E+01 0.1681462055E+01
61 1 0.6695006599E+01 0.6863779049E+01 0.6626959476E+00
62 1 0.7875496911E+01 0.7223398705E+01 0.2955894890E-02
63 1 0.4407622443E+01 0.8683432846E+01 0.1273866317E+02
64 1 0.1004598527E+01 0.8437076410E+01 0.1626373493E+01
65 1 0.1811895893E+01 0.9595510048E+01 0.1683962806E+01
66 1 0.2206696443E+01 0.1015717585E+02 0.2899207158E+01
67 1 0.1855265120E+01 0.9519105917E+01 0.4094182519E+01
68 1 0.1104196394E+01 0.8332976047E+01 0.4091529726E+01
69 1 0.6664953629E+00 0.7822140822E+01 0.2858343199E+01
70 1 0.4767595933E+00 0.7975095018E+01 0.3209252173E+00
71 1 0.9558927816E+01 0.5594886264E+01 0.5737980733E+01
72 1 0.1009662267E+02 0.6395162637E+01 0.4694339526E+01
73 1 0.1130547359E+02 0.6076565172E+01 0.4050602795E+01
74 1 0.1197492397E+02 0.4907705500E+01 0.4423267075E+01
75 1 0.1148058241E+02 0.4088924291E+01 0.5442028035E+01
76 1 0.1030009141E+02 0.4448498278E+01 0.6101791957E+01
77 1 0.8273652015E+01 0.5908455554E+01 0.6416565486E+01
78 1 0.1717094179E+02 0.5662145143E+01 0.4478346343E+01
79 1 0.1636364266E+02 0.6820575367E+01 0.4420757544E+01
80 1 0.1596883549E+02 0.7382227923E+01 0.3205512397E+01
81 1 0.1632025864E+02 0.6744143196E+01 0.2010539081E+01
82 1 0.1707132808E+02 0.5558017065E+01 0.2013188799E+01
83 1 0.1750904133E+02 0.5047200333E+01 0.3246379692E+01
84 1 0.1769881239E+02 0.5200205120E+01 0.5783791034E+01
85 1 0.6811739581E+01 0.8279388891E+01 0.1226310607E+02
86 1 0.7349471753E+01 0.7479132385E+01 0.1121946341E+02
87 1 0.8558336367E+01 0.7797768893E+01 0.1057576554E+02
88 1 0.9227746903E+01 0.8966646965E+01 0.1094846191E+02
89 1 0.8733370874E+01 0.9785400290E+01 0.1196722803E+02
90 1 0.7552880587E+01 0.9425780707E+01 0.1262696813E+02
91 1 0.1102075508E+02 0.7965746611E+01 -0.1087390418E+00
92 1 0.1442377874E+02 0.8212102870E+01 0.1100355083E+02
93 1 0.1361648139E+02 0.7053669198E+01 0.1094596153E+02
94 1 0.1322168076E+02 0.6492003386E+01 0.9730717191E+01
95 1 0.1357311202E+02 0.7130073388E+01 0.8535741855E+01
96 1 0.1432418071E+02 0.8316203241E+01 0.8538394654E+01
97 1 0.1476188189E+02 0.8827038435E+01 0.9771581124E+01
98 1 0.1495161773E+02 0.8674084284E+01 0.1230899907E+02
99 1 0.5869475301E+01 0.5504579845E+01 0.6891911436E+01
100 1 0.5331780486E+01 0.4704303514E+01 0.7935552661E+01
101 1 0.4122929621E+01 0.5022900996E+01 0.8579289445E+01
102 1 0.3453479290E+01 0.6191760673E+01 0.8206625125E+01
103 1 0.3947820802E+01 0.7010541846E+01 0.7187864118E+01
104 1 0.5128311738E+01 0.6650967799E+01 0.6528100144E+01
105 1 0.7154751105E+01 0.5191010550E+01 0.6213326728E+01
106 1 -0.1742538513E+01 0.5437320905E+01 0.8151545268E+01
107 1 -0.9352393849E+00 0.4278890650E+01 0.8209134094E+01
108 1 -0.5404321152E+00 0.3717238087E+01 0.9424379235E+01
109 1 -0.8918551469E+00 0.4355322912E+01 0.1061935253E+02
110 1 -0.1642924625E+01 0.5541448981E+01 0.1061670279E+02
111 1 -0.2080638046E+01 0.6052265644E+01 0.9383511944E+01
112 1 -0.2270409154E+01 0.5899260974E+01 0.6846100599E+01
113 2 0.6474081915E+01 0.3946202710E+01 0.2837118280E+01
114 2 0.6143076913E+01 0.4273987413E+00 0.3508510629E+00
115 2 0.4399721536E+01 0.3966833288E+01 0.1203354012E+02
116 2 0.2833555917E+01 0.5498913874E+01 0.2911663679E+01
117 2 0.8315400147E+00 0.2285843382E+01 0.5025554516E+01
118 2 -0.4574100361E+01 0.1531098540E+01 0.1292863625E+02
119 2 0.1170146294E+02 0.1171375883E+01 0.3267584212E+01
120 2 0.1203254380E+02 0.8751984031E+01 0.5753843583E+01
121 2 0.8281685068E+01 0.1191669931E+01 0.7121842218E+01
122 2 0.1534201242E+02 0.2723954310E+01 0.3192996940E+01
123 2 0.1734397819E+02 0.1061030193E+02 0.1079166034E+01
124 2 0.1725545685E+02 0.9855532342E+01 0.6226461953E+01
125 2 0.8954347798E+01 0.1603549977E+01 0.9792741627E+01
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127 2 0.1102870843E+02 0.1582919744E+01 0.5963199117E+00
128 2 0.1259487364E+02 0.5083885537E-01 0.9718196528E+01
129 2 0.1459688944E+02 0.3263909345E+01 0.7604305663E+01
130 2 0.2000253010E+02 0.4018654236E+01 -0.2987761298E+00
131 2 0.3726940437E+01 0.9928089801E+01 0.9362307670E+01
132 2 0.3395859193E+01 0.2347482076E+01 0.6876049092E+01
133 2 0.7146717964E+01 0.9907796511E+01 0.5508049595E+01
134 2 0.8639091740E-01 0.8375511592E+01 0.9436894769E+01
135 2 -0.1915574634E+01 0.4891640689E+00 0.1155072563E+02
136 2 -0.1827053556E+01 0.1243933697E+01 0.6403429800E+01
137 2 0.6474055709E+01 0.9495916087E+01 0.2837150296E+01
138 2 0.6143050770E+01 0.5977112048E+01 0.3508831015E+00
139 2 0.4399695354E+01 0.9516546608E+01 0.1203357230E+02
140 2 0.2833529760E+01 0.1104862713E+02 0.2911695733E+01
141 2 0.8315138446E+00 0.7835556664E+01 0.5025586600E+01
142 2 -0.4574126548E+01 0.7080811816E+01 0.1292866832E+02
143 2 0.1170143671E+02 0.6721089528E+01 0.3267616490E+01
144 2 0.1203257002E+02 0.3202270801E+01 0.5753811288E+01
145 2 0.8281658911E+01 0.6741383157E+01 0.7121874315E+01
146 2 0.1534198626E+02 0.8273667657E+01 0.3193028990E+01
147 2 0.1734400436E+02 0.5060588659E+01 0.1079133915E+01
148 2 0.1725548299E+02 0.4305819088E+01 0.6226429761E+01
149 2 0.8954321550E+01 0.7153263216E+01 0.9792773734E+01
150 2 0.9285326812E+01 0.1067206724E+02 0.1227904075E+02
151 2 0.1102868219E+02 0.7132632908E+01 0.5963518822E+00
152 2 0.1259484741E+02 0.5600552118E+01 0.9718228624E+01
153 2 0.1459686318E+02 0.8813622570E+01 0.7604337744E+01
154 2 0.2000250385E+02 0.9568367488E+01 -0.2987440616E+00
155 2 0.3726966525E+01 0.4378376722E+01 0.9362275815E+01
156 2 0.3395833117E+01 0.7897195320E+01 0.6876080997E+01
157 2 0.7146744136E+01 0.4358083041E+01 0.5508017805E+01
158 2 0.8641710225E-01 0.2825798329E+01 0.9436862585E+01
159 2 -0.1915600859E+01 0.6038877367E+01 0.1155075769E+02
160 2 -0.1827079760E+01 0.6793647021E+01 0.6403461875E+01
161 3 0.8753583692E+01 0.4832433075E+01 0.1817481304E+01
162 3 0.4969262268E+01 0.1709882876E+01 0.2324813961E+01
163 3 0.2787099191E+01 0.8335156825E+00 0.1194133208E+02
164 3 0.2280469686E+01 0.4668666201E+01 0.4601422566E+00
165 3 0.2255743976E+01 0.4604320010E+01 0.5326842661E+01
166 3 -0.1725734689E+00 0.1085100423E+01 0.2876488949E+01
167 3 0.9421979070E+01 0.2057553891E+01 0.4287325802E+01
168 3 0.1320630447E+02 0.1003454195E+02 0.3779903915E+01
169 3 0.9894188003E+01 0.9157928262E+01 0.7213758389E+01
170 3 0.1589509879E+02 0.1893719254E+01 0.5644514851E+01
171 3 0.1591978809E+02 0.1829346210E+01 0.7778302858E+00
172 3 0.1834814355E+02 0.9409618050E+01 0.3228244113E+01
173 3 0.6674845857E+01 0.7173199145E+00 0.1081237871E+02
174 3 0.1045916733E+02 0.3839870016E+01 0.1030504568E+02
175 3 0.1264133063E+02 0.4716237082E+01 0.6885277062E+00
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178 3 0.1560100340E+02 0.4464652075E+01 0.9753370950E+01
179 3 0.6006424545E+01 0.9041912374E+01 0.8342565873E+01
180 3 0.2222098939E+01 0.1064923986E+01 0.8849988478E+01
181 3 0.5534215095E+01 0.1941537722E+01 0.5416133604E+01
182 3 -0.4666956496E+00 0.9205746584E+01 0.6985376870E+01
183 3 -0.4913847623E+00 0.9270120145E+01 0.1185206161E+02
184 3 -0.2919740335E+01 0.1689847772E+01 0.9401647894E+01
185 3 0.8753557549E+01 0.1038214633E+02 0.1817513503E+01
186 3 0.4969236059E+01 0.7259596165E+01 0.2324846005E+01
187 3 0.2787073032E+01 0.6383229149E+01 0.1194136407E+02
188 3 0.2280443457E+01 0.1021837950E+02 0.4601743315E+00
189 3 0.2255717854E+01 0.1015403323E+02 0.5326874746E+01
190 3 -0.1725996660E+00 0.6634813709E+01 0.2876521030E+01
191 3 0.9421952732E+01 0.7607267155E+01 0.4287357997E+01
192 3 0.1320633073E+02 0.4484828890E+01 0.3779871723E+01
193 3 0.9894214284E+01 0.3608214836E+01 0.7213726075E+01
194 3 0.1589507262E+02 0.7443432594E+01 0.5644546933E+01
195 3 0.1591976200E+02 0.7379059542E+01 0.7778623547E+00
196 3 0.1834816966E+02 0.3859904752E+01 0.3228211982E+01
197 3 0.6674819754E+01 0.6267033117E+01 0.1081241086E+02
198 3 0.1045914117E+02 0.9389583282E+01 0.1030507782E+02
199 3 0.1264130438E+02 0.1026595033E+02 0.6885598171E+00
200 3 0.1314793402E+02 0.6430799668E+01 0.1216975003E+02
201 3 0.1317265945E+02 0.6495146304E+01 0.7303049469E+01
202 3 0.1560097713E+02 0.1001436538E+02 0.9753403026E+01
203 3 0.6006450540E+01 0.3492199087E+01 0.8342534128E+01
204 3 0.2222072654E+01 0.6614637435E+01 0.8850020549E+01
205 3 0.5534188920E+01 0.7491250930E+01 0.5416165845E+01
206 3 -0.4666695097E+00 0.3656033291E+01 0.6985344719E+01
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209 4 0.9664446690E+01 0.5286912073E+01 0.1165749139E+01
210 4 0.8277026409E+01 0.5450361360E+01 0.2855486300E+01
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212 4 0.4728074963E+01 0.5268663943E+00 0.2365632228E+01
213 4 0.2339832990E+01 -0.3863819108E+00 0.1196236277E+02
214 4 0.3481698681E+01 0.1264565560E+01 0.1106064022E+02
215 4 -0.3143912420E+01 0.4027273677E+01 0.1249161193E+02
216 4 0.2651640319E+01 0.5907627972E+01 0.5355512828E+00
217 4 0.2280162040E+01 0.3999813196E+01 0.6370111157E+01
218 4 0.2555107337E+01 0.5865971802E+01 0.5240236716E+01
219 4 -0.7193837066E+00 0.7499545286E+00 0.3898602270E+01
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221 4 0.8511169952E+01 0.2512027982E+01 0.4939129079E+01
222 4 0.9898482760E+01 0.2675495762E+01 0.3249302792E+01
223 4 0.1398467595E+02 0.1094034539E+02 0.3301442386E+01
224 4 0.1344758361E+02 0.8851544424E+01 0.3739125202E+01
225 4 0.1034155119E+02 0.7938064035E+01 0.7192713406E+01
226 4 0.9199506989E+01 0.9588898338E+01 0.8094420636E+01
227 4 0.1582508765E+02 0.1252224582E+01 0.6663402723E+01
228 4 0.1552400930E+02 0.3132704803E+01 0.5569139375E+01
229 4 0.1589541217E+02 0.1224862753E+01 -0.2654527027E+00
230 4 0.1562033107E+02 0.3090973287E+01 0.8644727764E+00
231 4 0.1889489929E+02 0.9074426392E+01 0.2206116327E+01
232 4 0.1842725358E+02 0.8716592545E+01 0.4320855550E+01
233 4 0.5763982984E+01 0.2628410350E+00 0.1146411113E+02
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