[CP2K-user] Errors when modifying restart file to simulaiton the deposition process
Dr. Zhiyin Gan
ganz... at gmail.com
Thu Jan 9 05:24:57 UTC 2020
Dear All :
I am trying to perform MD to simulate the deposition process of Al atom and
O atom, the substrate is Al2O3. The NVT ensemble is applied. The deposited
process is simulated by periodically inserting a certain atom (Al or O)
into the simulation box after running a certain steps (eg: 5000 steps) by
modifying the last RESTART file and restart the calculation by running cp2k
restart command using the restart file. When the first atom is inserted
into the box in the RESTART file for test running , the error occurs,
which is shown below, could anyone help to solve this?
The inp file and restart file are shown below. Can anyone help me?
Thank you for your time!
[image: 1.png]
#########################inp file#########################
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
&CHARGE
ATOM AL
CHARGE 1.2
&END CHARGE
&CHARGE
ATOM O
CHARGE -0.8
&END CHARGE
&NONBONDED
&WILLIAMS
atoms AL AL
A 2.518e14
B 10.925
C 20.13e5
RCUT 8.5
&END WILLIAMS
&WILLIAMS
atoms AL O
A 128.7e8
B 8.35
C .005e6
RCUT 8.5
&END WILLIAMS
&WILLIAMS
atoms O O
A 1.136e7
B 2.76
C 2.023e6
RCUT 8.5
&END WILLIAMS
&END NONBONDED
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA 0.41176
GMAX 10 20 100
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
A 4.7589998245 0.0000000000 0.0000000000
B 0.0000000000 8.2427997589 0.0000000000
C 0.0000000000 0.0000000000 50 #12.9910001755
&END CELL
&COORD
O 0.7281300000 6.9816500000 3.2477500000
O 3.1679647341 2.8449761031 3.2180937267
O 0.7242659597 1.5394673986 7.6373394530
O 3.0869179370 5.6713612199 7.6730381945
O 0.7928513302 4.2430226993 12.1470634990
O 3.1926946854 0.0525049711 11.9180407443
O 0.7110978266 1.2915618795 3.2588687814
O 3.1079692043 5.4498219751 3.3028321551
O 0.7204371442 4.0849501450 7.6648639751
O 3.0783549712 8.1929732976 7.7005582101
O 0.6397769406 6.8476338338 12.0851201372
O 3.1225789810 2.7213724135 11.9192491038
O 0.9671096629 4.1616340296 3.2720201749
O 3.2958738761 0.0586332288 3.2214467155
O 0.9420460055 6.9074282276 7.6367934370
O 3.3098249211 2.7938490020 7.6639095151
O 0.8557174733 1.3029174889 12.1967163081
O 3.2781799826 5.4437325654 12.1676042235
O 1.6502571764 5.4242054922 9.8834636203
O 3.9763211547 1.3385122141 9.8643063033
O 1.6061931212 8.1995298640 1.0696595111
O 4.0187446249 4.0668223212 1.1217727267
O 1.6646396776 2.6677039650 5.5044698240
O 4.0427907887 6.8009328927 5.4306912028
O 1.6562243258 2.8742898637 9.8480403280
O 4.0322655962 6.9471474232 9.8395701527
O 1.7203609105 5.5631802120 1.0558825984
O 4.0935545777 1.4365138741 0.8956151189
O 1.6463652059 0.1611020148 5.4457192714
O 4.0317667759 4.2794028387 5.4227729757
O 1.4484610667 8.3209177492 9.7575815724
O 3.8080246414 4.1649697216 9.8721405723
O 1.6010973599 2.8432047972 1.0779450577
O 3.8374274372 6.8754093163 1.0309346215
O 1.4730788651 5.5625061198 5.4623339149
O 3.8263616940 1.4525929549 5.4264055497
Al -0.0113699933 0.0452375213 4.5925640028
Al 2.3714902617 4.1344067192 4.6281186173
Al -0.0024531866 2.7935949087 8.9859749017
Al 2.3622933494 6.8993534655 9.0004890517
Al 0.0366704669 5.5048852599 0.8373850321
Al 2.4561825083 1.3626927798 0.7392674094
Al -0.0099091157 0.0009001890 1.8867395507
Al 2.4250581447 4.1810878894 1.9823609635
Al -0.0061572126 2.8155299229 6.3010642533
Al 2.4066136128 6.9388924747 6.3019334298
Al -0.0031912603 5.4895516598 10.8982508330
Al 2.3101365902 1.3864936726 10.8660155462
Al -0.0153222391 0.0445647966 8.4896091807
Al 2.3781842300 4.1654447039 8.5029846829
Al -0.0558973484 2.7829842557 12.3368301861
Al 2.3456220182 6.8576350501 12.2880544584
Al 0.0291719471 5.5230985256 4.1279716622
Al 2.3677270875 1.4214984887 4.1314449321
Al 0.0424300506 0.0398464253 11.1097531881
Al 2.3549648112 4.1716377776 11.2014283475
Al 0.0805638229 2.7681748826 2.2398208298
Al 2.3781477031 6.8971203480 2.2506108284
Al -0.0221075583 5.5379136555 6.8061981851
Al 2.3970377027 1.4112871616 6.8210583313
&END COORD
&END SUBSYS
STRESS_TENSOR ANALYTICAL
&END FORCE_EVAL
&GLOBAL
PROJECT al2o3
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 5000
TIMESTEP 0.1
TEMPERATURE 300.0
&THERMOSTAT
REGION GLOBAL
&NOSE
LENGTH 1
YOSHIDA 3
TIMECON 10000.
MTS 100
&END NOSE
&END THERMOSTAT
&END MD
&PRINT
&RESTART
&EACH
MD 50
&END
&END
&END
&END MOTION
#############################restart file##############################
# Version information for this restart file
# current date 2020-01-08 22:13:35.359
# current working dir
/home/dell/Documents/zhanglibin/program/Python/insert_atoms-3
# Program compiled at 2019年 07月 07日 星期日 07:43:07 CST
# Program compiled on
dell-PowerEdge-T630
# Program compiled for
local
# Source code revision number
svn:18464
&GLOBAL
PROJECT_NAME al2o3
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 5000
TIMESTEP 9.9999999999999992E-02
STEP_START_VAL 5000
TIME_START_VAL 5.0000000000002660E+02
ECONS_START_VAL -1.2895603149249308E+01
TEMPERATURE 3.0000000000000000E+02
&THERMOSTAT
REGION GLOBAL
&NOSE
LENGTH 1
YOSHIDA 3
TIMECON 9.9999999999999982E+03
MTS 100
&COORD
4.4929101034043538E-03
&END COORD
&VELOCITY
2.5968167624076281E-07
&END VELOCITY
&MASS
2.8740019641650124E+10
&END MASS
&FORCE
3.3308416588440516E-12
&END FORCE
&END NOSE
&END THERMOSTAT
&AVERAGES T
&RESTART_AVERAGES
ITIMES_START 1
AVECPU 8.4568950926942853E-03
AVEHUGONIOT 0.0000000000000000E+00
AVETEMP_BARO 0.0000000000000000E+00
AVEPOT -1.3034862008742211E+01
AVEKIN 1.3821606127227268E-01
AVETEMP 4.9316528907100150E+02
AVEKIN_QM 0.0000000000000000E+00
AVETEMP_QM 0.0000000000000000E+00
AVEVOL 1.3236008873879447E+04
AVECELL_A 8.9932063347558096E+00
AVECELL_B 1.5576634112536917E+01
AVECELL_C 9.4486306644281882E+01
AVEALPHA 9.0000000000000000E+01
AVEBETA 9.0000000000000000E+01
AVEGAMMA 9.0000000000000000E+01
AVE_ECONS -8.3422075825544482E-03
AVE_PRESS 3.8989536528213948E+03
AVE_PXX 1.0752360571496547E+04
&END RESTART_AVERAGES
&END AVERAGES
&END MD
&PRINT
&RESTART SILENT
&EACH
MD 50
&END EACH
&END RESTART
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD FIST
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
&NONBONDED
&WILLIAMS
ATOMS AL AL
A 2.5180000000000000E+14
B 1.0925000000000001E+01
C 2.0129999999999998E+06
RCUT 8.5000000000000000E+00
&END WILLIAMS
&WILLIAMS
ATOMS AL O
A 1.2870000000000000E+10
B 8.3499999999999996E+00
C 5.0000000000000000E+03
RCUT 8.5000000000000000E+00
&END WILLIAMS
&WILLIAMS
ATOMS O O
A 1.1360000000000002E+07
B 2.7599999999999998E+00
C 2.0230000000000002E+06
RCUT 8.5000000000000000E+00
&END WILLIAMS
&END NONBONDED
&CHARGE
ATOM AL
CHARGE 1.2000000000000000E+00
&END CHARGE
&CHARGE
ATOM O
CHARGE -8.0000000000000004E-01
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA 4.1176000000000001E-01
GMAX 10 20 100
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
A 4.7589998245000000E+00 0.0000000000000000E+00
0.0000000000000000E+00
B 0.0000000000000000E+00 8.2427997589000004E+00
0.0000000000000000E+00
C 0.0000000000000000E+00 0.0000000000000000E+00
5.0000000000000007E+01
MULTIPLE_UNIT_CELL 1 1 1
&END CELL
&COORD
O 8.1538769817395507E-01 7.1421510807510522E+00
3.1735736208844640E+00
O 3.0361789112662394E+00 2.7778093578782843E+00
3.0066437249544977E+00
O 8.0353416439540881E-01 1.5128590920442921E+00
7.6386384724585774E+00
O 3.2342937442147588E+00 5.4975327112861727E+00
7.6781506890676647E+00
O 5.8225821465176519E-01 3.8072930011024164E+00
1.1898545715053386E+01
O 3.4133390833648858E+00 3.7401484612820596E-01
1.2209764506552022E+01
O 7.3551457785801000E-01 1.4058173150577216E+00
3.2549867248552680E+00
O 3.1213410649855327E+00 5.4913312195586066E+00
3.0238108761218467E+00
O 6.9757949337773362E-01 3.9842886533631292E+00
7.6358537936397370E+00
O 3.1867908752222855E+00 8.0924641978288108E+00
7.8336087949048423E+00
O 6.3713865396409730E-01 6.6759081374002536E+00
1.2205820720592147E+01
O 2.8311851208042111E+00 2.8930454374893979E+00
1.2350521831113561E+01
O 8.8796278487252500E-01 4.2815188440500371E+00
3.0797874405844539E+00
O 3.3424545398655630E+00 1.2837347922353551E-01
3.1772017488935953E+00
O 1.0620775099228983E+00 6.7920184936688841E+00
7.7129840519054618E+00
O 3.3391080441017524E+00 2.7184388588122417E+00
7.6333325324016599E+00
O 1.0416611054464928E+00 9.9503364918010573E-01
1.2395293393974267E+01
O 2.9728156920557871E+00 5.5697752105478306E+00
1.2365320708269641E+01
O 1.5468848221227602E+00 5.3345334762849799E+00
9.9258702001644767E+00
O 4.0386165014964996E+00 1.3706527976165135E+00
1.0090144993577862E+01
O 1.8308325640197713E+00 8.7675874017928965E+00
1.1115187907360660E+00
O 3.6361724920244147E+00 3.8582580701707312E+00
9.5833667992109162E-01
O 1.5763505488122860E+00 2.7601647195470078E+00
5.4239151887436119E+00
O 4.0063773368183382E+00 6.7909278530808370E+00
5.3061761849774332E+00
O 1.6016430376728588E+00 2.7244758209786331E+00
9.9507354551411797E+00
O 4.1185441985682010E+00 6.8836456771479693E+00
1.0068073796181714E+01
O 1.4579221558106303E+00 5.7983294577856226E+00
1.0439713016841581E+00
O 4.2317728268673331E+00 1.2783657883440462E+00
6.3808164783994425E-01
O 1.5981502356529846E+00 1.2018740351779615E-01
5.4297528725640340E+00
O 3.9572441489842554E+00 4.1297030515914246E+00
5.2593017856377591E+00
O 1.6022168300348276E+00 8.2409386453044124E+00
9.9650758027119632E+00
O 3.7997303081999112E+00 4.0060759059753446E+00
9.8822486650099588E+00
O 1.2246713215214897E+00 3.2498520063740832E+00
8.6903890340672263E-01
O 4.0417893542633987E+00 7.0132461649250750E+00
1.0597643389525204E+00
O 1.5194229482482271E+00 5.5647360879990009E+00
5.2969821766957690E+00
O 3.8177869764668091E+00 1.3653612995893953E+00
5.4330232506360083E+00
Al 1.4148282345211783E-02 8.5009190302278145E-02
4.4311321751095063E+00
Al 2.2928966293009010E+00 4.0659507999084665E+00
4.3801466640510833E+00
Al -1.2168465793944057E-03 2.8021670887342367E+00
8.8898636923989667E+00
Al 2.6009148687446526E+00 6.7115814211404832E+00
8.9806771714130385E+00
Al -1.9434971277155999E-01 5.2938109799981614E+00
1.5307361417043555E+00
Al 2.6626399819753073E+00 2.1700244760018079E+00
6.4362977809919197E-01
Al 2.7307277075103875E-01 1.2367130447654130E-01
1.8739886626820061E+00
Al 2.2276937236565448E+00 4.3500065487517716E+00
1.8363026666112665E+00
Al 8.1633552834300890E-03 2.8414411843338678E+00
6.3766380556785034E+00
Al 2.4737357060138239E+00 6.6700318065722950E+00
6.4137374457464338E+00
Al -3.7288913255992581E-02 5.4140308912480641E+00
1.1059083564207269E+01
Al 2.3913715997215048E+00 1.4409618585886730E+00
1.1131930247510473E+01
Al 2.5049460142282531E-01 1.3905100715134955E-01
8.6569009003102586E+00
Al 2.2888355081046359E+00 3.9058469629932526E+00
8.6908729457034752E+00
Al -3.7299080784877009E-01 2.1025159868949310E+00
1.2202819922470376E+01
Al 2.1991941613411625E+00 7.4020115253068255E+00
1.2579467316547628E+01
Al -9.1056878517587606E-02 5.5524259467668751E+00
4.0983262002353049E+00
Al 2.4124741260952050E+00 1.4043199241595739E+00
4.1581811035287846E+00
Al 2.6722741210550194E-01 -6.3522243375827195E-02
1.1187567941055391E+01
Al 2.3583910139033710E+00 4.2560751940752723E+00
1.1148187849014626E+01
Al 6.9787124823122465E-02 2.4568859445369609E+00
1.9084168648931690E+00
Al 2.3381700410585458E+00 7.2181739561473783E+00
1.8851316702078256E+00
Al 1.1074419912610499E-01 5.5230075602613509E+00
6.6222287944227123E+00
Al 2.3746453520279243E+00 1.4101783747752916E+00
6.6131355282229967E+00
O 0.2312752625376069 1.1343035619292914 50 #one atom
added
&END COORD
&VELOCITY
5.1875045922156276E-05 -3.4310741681474437E-05
1.7861469879547549E-04
2.4253131130780491E-04 3.3475886500034045E-04
-4.8854756036451926E-05
-1.1410975560011851E-04 1.0225530256591602E-04
8.4821943489379336E-05
1.1681835296228760E-04 -1.2352479556692765E-04
2.8826107404801273E-04
4.3102303300290574E-04 1.8090992677997897E-04
1.6643411956830182E-04
-3.4769354728737394E-04 -1.8380654679487217E-04
-2.1400291115121901E-04
-2.1584257163886718E-04 2.9801589225294302E-04
7.3757220352222124E-05
4.7756224179359810E-05 2.0301427594322669E-04
3.1970850296907849E-05
1.0460165559975634E-06 -3.8670782061857995E-04
-5.0871419143011011E-04
2.2689242941003446E-04 2.9805735664245565E-04
-4.2230329047369199E-04
6.1881415476247646E-04 1.9372521042636649E-05
-3.1214454563819124E-05
7.6551391783590480E-05 -2.2803487327509176E-04
6.4143959573777749E-05
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1.8413796352434792E-04
3.3573440829235947E-04 -2.1436205783490996E-04
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-8.6206483566880421E-05 2.4117455687950500E-04
1.8795381779985879E-04
2.5276312480754053E-04 -1.0096678297079364E-04
3.1492946212155400E-04
1.9108921710739925E-04 -1.9131175373491552E-04
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1.8020009310761218E-05 -2.3546754588191918E-04
-1.0449029404271647E-04
-1.3687571494859103E-05 7.1477467497327410E-05
-5.5996081332463656E-05
-5.0346662152787931E-05 -2.1790940356861051E-04
-4.3829398456262820E-05
-2.4573827836861571E-04 -1.0272323465931772E-04
-1.3788391681506250E-04
9.6117516307979810E-05 -2.2373444995655664E-04
-5.3094130317377010E-05
0 0 -10 #one atom added
&END VELOCITY
&TOPOLOGY
NUMBER_OF_ATOMS 61
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
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