atomes go far away from box in NVT simulation
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tao liu
Jan 29, 2016, 4:08:52 AM1/29/16
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Hi all,
I am running a NVT MD simulation and use the coordinates and velocities of the atoms from CP2K. I am using v2.7 CP2K on ARCHER on MgSiO3 (240 atoms).
All of the atoms are in and around the simulation box in the initial model, but the atoms are moving out of the box along the simulation time, and go far away from the box gradually, You can see that the 'z' coordinate of the first atom changes from 3.04 (0 ps) to -105 (75 ps). I know it is a periodic box, it doesn't mater where the atoms are, but it is a very strange looking . Is there any keyword to restrict atoms just moving around the simulation box (except to freeze a atom)? Thanks.
Here is my input file
&GLOBAL
PROJECT pv-lad
RUN_TYPE md
PRINT_LEVEL low
&END GLOBAL
&MOTION
&PRINT
&STRESS
&END STRESS
&velocities
&end velocities
&END PRINT
&MD
ENSEMBLE NVT
STEPS 10001
TIMESTEP 1
TEMPERATURE 4000.0
&THERMOSTAT
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 10.0
MTS 2
&END NOSE
&END
&END MD
&END MOTION
&FORCE_EVAL
METHOD Quickstep
STRESS_TENSOR analytical
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 500
REL_CUTOFF 40
&END MGRID
&PRINT
&DFT_CONTROL_PARAMETERS
&END DFT_CONTROL_PARAMETERS
&END PRINT
&QS
ls_scf
EPS_DEFAULT 1.0E-10
EXTRAPOLATION use_prev_p
MAP_CONSISTENT
&END QS
&LS_SCF
PURIFICATION_METHOD TRS4
MU 0.15
MAX_SCF 200
S_PRECONDITIONER ATOMIC
&END
&SCF
&OT ON
MIXED_PRECISION .TRUE.
&END OT
EPS_SCF 1.0E-5
MAX_SCF 200
SCF_GUESS atomic
&OUTER_SCF
EPS_SCF 1.0E-7
MAX_SCF 500
&END
&END SCF
&XC
&XC_FUNCTIONAL LDA
&END XC_FUNCTIONAL
&END XC
&END DFT
&PRINT
&STRESS_TENSOR
NDIGITS 4
&END STRESS_TENSOR
&END PRINT
&SUBSYS
&CELL
ABC 26.0369999999999990 9.1050000000000004 6.2900000000000000
MULTIPLE_UNIT_CELL 1 1 1
SYMMETRY ORTHORHOMBIC
&END CELL
&COORD
Mg -8.5841870397562470E-02 2.4446737869627219E-01 4.8382391457694479E-01
Mg 2.6031406086949271E-01 2.6092719343831572E-01 4.4217146672191654E-01
Mg 5.8328369689563009E-01 2.7457651320156096E-01 5.4373784721259688E-01
Mg -1.6551265244923527E-01 5.0062949446903793E-01 4.1425269983661733E-01
Mg 1.7504514944695440E-01 4.8334791029082946E-01 5.1221241800498718E-01
Mg 5.0100847251823832E-01 5.1467931925712862E-01 5.3871665439449057E-01
Mg 4.9696258783467661E-03 2.8564556687435058E-02 -5.5635394771647945E-02
Mg 3.3341069514857558E-01 4.3041475940459976E-02 7.2042674649568979E-03
Mg 6.6442011772974674E-01 7.8685228117939057E-02 -1.2914007205212010E-02
Mg -8.8965855464970933E-02 3.0757986909734858E-01 -1.7341304196210550E-02
Mg 2.6429480997107940E-01 2.9871264106622647E-01 -1.1588724444114285E-04
Mg 5.9663827162760652E-01 3.2436772679716008E-01 1.4053134928836836E-03
Mg 8.3963502182136829E-02 2.2560437235288969E-01 4.5755778075376385E-01
Mg 4.1680405569713747E-01 2.5279272185825119E-01 5.1166415618287830E-01
Mg 7.5782180365131513E-01 2.5740119746015044E-01 5.0321085850400704E-01
Mg 1.0012635472290692E-02 4.9177815625580329E-01 5.0542111791271982E-01
Mg 3.4826208963496036E-01 4.9244069485338821E-01 5.3543844342620606E-01
Mg 6.7617022771933921E-01 4.9093655765936467E-01 4.3813890750518381E-01
Mg -1.7218244414747880E-01 5.5919241943238295E-02 -3.0553492021523139E-02
Mg 1.7385353536448078E-01 8.1253409311228611E-03 5.9398609267433799E-03
Mg 5.0334906666302892E-01 4.1457643446633649E-02 3.8409145603852696E-02
Mg 9.0018318897402805E-02 3.0490848749171917E-01 2.4777148653723682E-02
Mg 4.2759112826818119E-01 3.3550241386878465E-01 2.3574288059742265E-02
Mg 7.6029010663652807E-01 3.1034820319365952E-01 -7.7023048895912327E-02
Mg -8.1313873877322862E-02 7.7313009491039986E-01 4.3461633154845569E-01
Mg 2.4331569943035028E-01 7.3221060103160474E-01 5.1839726066449121E-01
Mg 5.9219372315569052E-01 7.2690449382934397E-01 4.9708940180974087E-01
Mg -1.5023352778399374E-01 9.9804254663294489E-01 4.6895512817445412E-01
Mg 1.7747341524146643E-01 9.8395743227503896E-01 5.3463993730437831E-01
Mg 5.0519021038414380E-01 1.0007092110747235E+00 5.0046645715607063E-01
Mg -2.2470938063514673E-03 5.5717466274186511E-01 -2.4260363411724203E-02
Mg 3.3247183757664761E-01 5.7859926774950377E-01 -1.8963323628777000E-02
Mg 6.6710460915604308E-01 5.4711297978742368E-01 -1.8744795300869112E-02
Mg -6.9702901123363123E-02 8.1471277075959991E-01 -1.3694208100214843E-02
Mg 2.5266844568200930E-01 8.1442337341414928E-01 -3.0440293716887004E-03
Mg 5.9155869762889146E-01 8.0276564100592418E-01 2.8292242575817007E-03
Mg 8.5198439961117159E-02 7.2502463201591161E-01 4.7741023096073743E-01
Mg 4.2797150764181374E-01 7.3183873081787887E-01 5.7055317612785195E-01
Mg 7.4627180458684039E-01 7.6710443821753282E-01 4.9709870301145453E-01
Mg -5.8810617600903881E-03 9.9267467333396797E-01 4.5006985665657040E-01
Mg 3.4547972080063727E-01 9.7433640024046786E-01 5.2063541360370935E-01
Mg 6.7069899018667600E-01 9.8999935891476076E-01 4.6416642311786444E-01
Mg 1.6619195913826168E-01 5.6494493718312333E-01 1.8350295635919005E-03
Mg 5.1023411830493037E-01 5.5831351058750600E-01 -3.8267644482570563E-02
Mg 8.3634339585256257E-01 5.5467337454304844E-01 7.8009284329952728E-03
Mg 8.4720040699066204E-02 7.7745794948872027E-01 -2.1561455207449107E-02
Mg 4.3489025913152479E-01 8.3641628928970846E-01 1.9941806566879525E-02
Mg 7.5419086823247095E-01 7.7190236576453275E-01 -2.5980926763719558E-02
Si -1.6728356246780929E-01 2.8232272664060165E-01 2.1558479386125443E-01
Si 1.7791388760609078E-01 2.7698111204688136E-01 2.7041876731432823E-01
Si 5.1440565600981436E-01 3.1896093411827270E-01 2.0620776655304177E-01
Si -7.5382514071711884E-02 4.1774027816088320E-02 2.0219155003479139E-01
Si 2.5642494482412936E-01 1.7623959610342122E-02 2.4932156137609984E-01
Si 5.8382910456387771E-01 2.9871433525202728E-02 2.4972175621105297E-01
Si -7.7283222438805949E-02 1.0036040156320534E+00 -2.8302178874664957E-01
Si 2.5899578237135035E-01 1.0285787167602245E+00 -2.7687563656782110E-01
Si 5.9156815965151488E-01 1.0223842301915391E+00 -2.6162822205629216E-01
Si -1.6517454406786483E-01 2.5635298362814551E-01 -2.6994044392031807E-01
Si 1.7939776418951683E-01 2.8464306969936548E-01 -2.5399808353232317E-01
Si 5.0542957339013084E-01 2.7111377918624624E-01 -2.9980422429052739E-01
Si 2.0323415780992295E-03 2.7779541789661716E-01 2.4671233314957591E-01
Si 3.4103948579684734E-01 2.6421176739814001E-01 2.5298110434427307E-01
Si 6.8278819590801654E-01 2.7528119667098000E-01 2.1297589505608711E-01
Si 8.5455304988850622E-02 1.0201354135682468E+00 2.4360345980615253E-01
Si 4.2441886884211777E-01 1.0582001614595029E+00 2.4545414981522820E-01
Si 7.6284723598227533E-01 1.0246937028042182E+00 2.3573758092393254E-01
Si 9.0434407921566901E-02 1.2080918715200891E-02 -2.5561808444944212E-01
Si 4.2539570597791759E-01 1.6024835047054074E-02 -2.4129761989223139E-01
Si 7.5361681011693626E-01 1.7345499591522894E-02 -2.4183432340715560E-01
Si 4.0214016112855768E-03 2.6733818264111503E-01 -2.5736571860243879E-01
Si 3.4325827442590690E-01 2.3718624650465039E-01 -2.5233475548346285E-01
Si 6.7377368672748161E-01 2.6802314483608120E-01 -2.8770164636283735E-01
Si -1.6438486662668073E-01 7.7925008023812892E-01 2.2749162278489696E-01
Si 1.6935052292611530E-01 7.6421962754004247E-01 2.5746508918875061E-01
Si 5.1195248976614460E-01 7.7270469269255471E-01 2.8921649405910033E-01
Si -8.1292853372605861E-02 5.2258636422540261E-01 2.1334993297416041E-01
Si 2.5586956978520836E-01 5.2541193405891462E-01 2.3064885447020086E-01
Si 5.9907922064845587E-01 5.2492735678963398E-01 2.3917225394417080E-01
Si -8.4039745698287482E-02 5.0821587002063040E-01 7.0708706469043636E-01
Si 2.5973751241889526E-01 5.2773505997819559E-01 7.5485919505089094E-01
Si 5.9026490822014377E-01 5.2198923213626380E-01 7.5916217382059015E-01
Si -1.6161104078241190E-01 7.5795256913335007E-01 7.1615013879434641E-01
Si 1.6405159065553662E-01 7.5605166953209457E-01 7.6075986266507178E-01
Si 5.1399989926238021E-01 7.8487713286195970E-01 7.8081696405594214E-01
Si 3.0782381080409833E-03 7.6679603512525851E-01 2.2173378897874271E-01
Si 3.4300414616440517E-01 7.7440867019748816E-01 2.5346626259022076E-01
Si 6.6847085118347582E-01 7.9502708574251402E-01 2.3379293196521375E-01
Si 8.6105585753538452E-02 5.0593505976705477E-01 2.2474077405524959E-01
Si 4.1928440039488601E-01 5.3202956831114900E-01 2.4888903862232040E-01
Si 7.5110104720354587E-01 5.1751414796081341E-01 1.8623319375503375E-01
Si 8.7010409134891040E-02 5.1721773980339680E-01 -2.7557788603381639E-01
Si 4.2653328985876254E-01 5.3829838819185472E-01 -2.5931663126388615E-01
Si 7.6046780906784672E-01 5.2758793161932660E-01 -3.1906772881526502E-01
Si 4.1308194014055086E-03 7.6158057861721695E-01 7.1485467908596856E-01
Si 3.4065455667555811E-01 7.7713559351274719E-01 7.6180820267965244E-01
Si 6.7216236348476732E-01 7.7659011774637643E-01 7.3094072544381705E-01
O -1.1878218813567269E-02 3.0552745818390664E-01 4.8280560072965090E-01
O 3.2534359022021714E-01 2.9856267054696761E-01 4.8739837981605194E-01
O 6.5459429717159567E-01 3.1354805498570237E-01 4.9667146459659384E-01
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O 7.8591937834212366E-01 1.7978256568609235E-01 1.5812532774263985E-01
O 1.4033667897801375E-01 4.1269811217451718E-01 1.6623174864260304E-01
O 4.7703720271037081E-01 4.4320864932387821E-01 1.6291797724779025E-01
O 8.0607253807035473E-01 4.2658611727491463E-01 1.7358981441861657E-01
O -3.0361172114472069E-02 9.1560731448497767E-01 -2.4644259974803873E-01
O 3.0693087908151084E-01 9.1075763435471757E-01 -2.0692296380238806E-01
O 6.3830974802852469E-01 9.2084972199968129E-01 -1.6933650874815112E-01
O -4.9914913727723650E-02 6.7187707262471830E-01 -2.5558759876898168E-01
O 2.8502502015620074E-01 6.8379280742634807E-01 -2.3416879455180786E-01
O 6.1912671101739747E-01 6.9293448326299911E-01 -2.1105026068616869E-01
O -1.0026969199538097E-01 8.9685040169349806E-01 2.5441771635546506E-01
O 2.2065626554037793E-01 8.7066278979515155E-01 3.2799645364169716E-01
O 5.6066187646605725E-01 8.7857542231317554E-01 3.3318049597205784E-01
O -1.2593518087356351E-01 6.3623473234896921E-01 2.8721679207213630E-01
O 1.9081139907637110E-01 6.1242409933442088E-01 2.8798907717818084E-01
O 5.4574916545356267E-01 6.1143623822325910E-01 3.3157783174048217E-01
O -1.3235302608873989E-01 6.0589610280050832E-01 6.4594063179307859E-01
O 2.0184794793124600E-01 6.3002767107121060E-01 6.6564174213650495E-01
O 5.4134357038271252E-01 6.2650800686889052E-01 6.9364237205592438E-01
O -1.1320028574200068E-01 8.8135564543997091E-01 6.4321680131118086E-01
O 2.3267359259702497E-01 8.6958215205690736E-01 6.8908445002615915E-01
O 5.6465432448155672E-01 8.7184700041293761E-01 7.0531628724810269E-01
O -4.2621863071148985E-02 6.6742492036733536E-01 1.2877140913861329E-01
O 2.8312696859637526E-01 6.8126505647660385E-01 2.0337281112138650E-01
O 6.2645648213341754E-01 6.8382565227601799E-01 1.9281505016717676E-01
O -2.8201529353336616E-02 9.3955251497686487E-01 1.5930196031901150E-01
O 3.1120446524539652E-01 9.3418556419764875E-01 2.2478527811333959E-01
O 6.3568880389072280E-01 9.5127884528921847E-01 1.7812471706357072E-01
O 1.4000287326271965E-01 9.0078179863766805E-01 -1.8057725352899179E-01
O 4.7877482715586267E-01 9.3468349595848255E-01 -1.8620470687685570E-01
O 8.0521723814498569E-01 9.2413756853942941E-01 -1.8865685801289381E-01
O 1.1991375229196477E-01 6.5435990256367171E-01 -1.8010093869470617E-01
O 4.6102352049016782E-01 6.7871313859137983E-01 -1.9419788233522678E-01
O 7.8454897234366106E-01 6.5781467249533421E-01 -2.5523916192427448E-01
O 5.1080723884232335E-02 8.6232040223900186E-01 2.9823849185823026E-01
O 3.9097593415316895E-01 8.6672780665133053E-01 3.5770099595791999E-01
O 7.2484142707316546E-01 8.6048126179126916E-01 2.5711140554384249E-01
O 4.1043349988371280E-02 6.0444622383396329E-01 2.9072778322645382E-01
O 3.6330695908740912E-01 5.9621360916061772E-01 2.8034067174190863E-01
O 7.0573859989380738E-01 6.1996589016319503E-01 2.4140898597504820E-01
O 3.8042391787087397E-02 6.0478757057803678E-01 7.0807746344902189E-01
O 3.7904786311879596E-01 6.4507384765468945E-01 6.9031586750440332E-01
O 6.9526818344367791E-01 6.2135571770171905E-01 6.6837106531584500E-01
O 5.9242655384482291E-02 8.4946237807199976E-01 6.8604253750850153E-01
O 3.9697151240540690E-01 8.6529496711891274E-01 7.3268176010280039E-01
O 7.1764945617944320E-01 8.9703279849916029E-01 6.7120232595711293E-01
O 1.1306310010342996E-01 6.7186534427512035E-01 1.8032770604537174E-01
O 4.5725920735762615E-01 6.8144900678307918E-01 2.1929015248337766E-01
O 7.9035777786540340E-01 6.5272523884954170E-01 1.6173703166177425E-01
O 1.2691336026982300E-01 8.8193897928857723E-01 1.5298022868968228E-01
O 4.6974258018389786E-01 9.4087896259039372E-01 2.4423433342220854E-01
O 8.0798182559559051E-01 9.1559411453756445E-01 1.6014252990802127E-01
SCALED T
&END COORD
&TOPOLOGY
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY
&KIND Mg
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q10
&END KIND
&KIND Si
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q6
&END KIND
&PRINT
&CELL
&END CELL
&KINDS
BASIS_SET
POTENTIAL
&END KINDS
&END PRINT
&END SUBSYS
&END FORCE_EVAL
initial coordinates (head of pos file) of the initial model
240
i = 0, time = 0.000, E = -5533.8818888693
Mg -2.2350647795 2.2258754830 3.0432524227
Mg 6.7777972029 2.3757420963 2.7812585257
Mg 15.1869576161 2.5000191527 3.4201110590
Mg -4.3094529318 4.5582315471 2.6056494820
Mg 4.5576505562 4.4008827232 3.2218161093
Mg 13.0447575990 4.6861552018 3.3885277561
Mg 0.1293941490 0.2600802886 -0.3499466331
Mg 8.6810142696 0.3918926384 0.0453148424
Mg 17.2995066053 0.7164290020 -0.0812291053
Mg -2.3164039787 2.8005147081 -0.1090768034
Mg 6.8814439672 2.7197785969 -0.0007289308
Mg 15.5346706784 2.9533681525 0.0088394219
Mg 2.1861577063 2.0541278103 2.8780384409
Mg 10.8523271982 2.3016777325 3.2183675424
Mg 19.7314063017 2.3436379029 3.1651963000
Mg 0.2606989898 4.4776401127 3.1790988317
Mg 9.0677000278 4.4836725266 3.3679078092
Mg 17.6054442191 4.4699773575 2.7558937282
Mg -4.4831142983 0.5091446979 -0.1921814648
coordinates after 20ps
240
i = 20001, time = 20001.000, E = -5534.1383369278
Mg -8.5212228136 -17.2329853845 -6.1595394457
Mg 0.1733030533 -17.2261286967 -6.2821580924
Mg 8.9959146485 -17.4095596792 -6.3696605785
Mg -10.5729449901 -14.6903815393 -5.8709632264
Mg -1.6408954749 -14.7889119922 -6.1154406061
Mg 7.0096825252 -15.0695676381 -6.2952011201
Mg -6.5462144938 -18.6352030196 -9.2394688534
Mg 2.7079580192 -19.2117381190 -9.0573553409
Mg 11.0703485543 -19.0039397574 -9.3380730778
Mg -8.2970565765 -16.4689058371 -9.2340818459
Mg 0.4952232634 -16.9586463739 -9.4256184855
Mg 9.2344598716 -16.8880682175 -9.2526558096
Mg -4.2037103591 -17.0867382294 -6.0038126867
Mg 4.9376923386 -16.7217767801 -6.2864741981
Mg 13.1878255020 -17.2638944927 -6.2403029009
Mg -6.0381312891 -14.7081735538 -6.3737176302
Mg 2.3822045804 -14.6944383387 -6.1485179972
Mg 11.4396035728 -14.8853543043 -6.3185200850
Mg -10.4231395906 -18.8180442052 -9.3533964840
Mg -2.0886701394 -18.8927968592 -9.5809690521
Mg 6.8530648011 -18.8965492739 -9.4719921566
Mg -4.0205717577 -16.5417084935 -9.1752344616
Mg 4.7672752630 -16.7706042565 -9.2988751763
Mg 13.2134011273 -16.7797712709 -9.4822572983
Mg -8.3513203967 -12.4424046604 -6.3338283428
Mg 0.1740399213 -12.6675128344 -6.0703348080
Mg 9.1188169422 -12.9013949048 -6.1136900038
Mg -10.3195768248 -10.1868043404 -6.1259349808
coordinates after 70ps
240
i = 75001, time = 75001.000, E = -5534.1134699400
Mg -29.9516376336 -15.1194881940 -105.6864548489
Mg -21.4511789621 -15.2926359800 -106.1107492361
Mg -12.3363043787 -15.5007476138 -106.2108320349
Mg -32.2417730367 -12.9827426855 -105.5340500595
Mg -23.4138501483 -12.4400416991 -106.1547836826
Mg -14.7562896521 -13.1941836426 -106.0632110738
Mg -27.8160910483 -16.6746036456 -109.2618664112
Mg -19.3826628235 -17.1830156386 -109.1795648209
Mg -10.5844317056 -16.9004665903 -109.1913904136
Mg -29.8214023359 -14.3215323946 -109.1082157156
Mg -21.3262188298 -14.6000591188 -109.3459316789
Mg -12.5883003718 -14.7171299129 -108.9683410866
Mg -25.8265527209 -14.9827801002 -106.1365938986
Mg -17.1148136255 -15.5361901256 -105.8236732361
Mg -8.4142552222 -15.0898366321 -106.0625881355
Mg -27.5560141815 -12.8040524795 -105.9702759551
Mg -19.0600590386 -13.1822114701 -105.8094803560
Mg -10.3985974837 -12.9584366337 -106.0224361393
Mg -32.3640441320 -16.7883161725 -108.8004958341
Mg -23.7100783179 -16.5857359895 -109.1708486711
Mg -14.7782068474 -17.3885317222 -109.0902597143
Mg -25.3286013327 -14.4648690199 -109.0576491752
Mg -16.8045905059 -15.0924280776 -109.2360875952
Mg -8.0511065290 -14.4302778422 -108.8879246410
Mg -30.0144113017 -10.4071856423 -105.7877594307
Mg -21.3870390974 -10.6425949879 -106.0301613661
Mg -12.5339204264 -10.8533353879 -105.9856478294
I am running a NVT MD simulation and use the coordinates and velocities of the atoms from CP2K. I am using v2.7 CP2K on ARCHER on MgSiO3 (240 atoms).
All of the atoms are in and around the simulation box in the initial model, but the atoms are moving out of the box along the simulation time, and go far away from the box gradually, You can see that the 'z' coordinate of the first atom changes from 3.04 (0 ps) to -105 (75 ps). I know it is a periodic box, it doesn't mater where the atoms are, but it is a very strange looking . Is there any keyword to restrict atoms just moving around the simulation box (except to freeze a atom)? Thanks.
Here is my input file
&GLOBAL
PROJECT pv-lad
RUN_TYPE md
PRINT_LEVEL low
&END GLOBAL
&MOTION
&STRESS
&END STRESS
&velocities
&end velocities
&END PRINT
&MD
ENSEMBLE NVT
STEPS 10001
TIMESTEP 1
TEMPERATURE 4000.0
&THERMOSTAT
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 10.0
MTS 2
&END NOSE
&END
&END MD
&END MOTION
&FORCE_EVAL
METHOD Quickstep
STRESS_TENSOR analytical
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 500
REL_CUTOFF 40
&END MGRID
&DFT_CONTROL_PARAMETERS
&END DFT_CONTROL_PARAMETERS
&END PRINT
&QS
ls_scf
EPS_DEFAULT 1.0E-10
EXTRAPOLATION use_prev_p
MAP_CONSISTENT
&END QS
&LS_SCF
PURIFICATION_METHOD TRS4
MU 0.15
MAX_SCF 200
S_PRECONDITIONER ATOMIC
&END
&SCF
&OT ON
MIXED_PRECISION .TRUE.
&END OT
EPS_SCF 1.0E-5
MAX_SCF 200
SCF_GUESS atomic
&OUTER_SCF
EPS_SCF 1.0E-7
MAX_SCF 500
&END
&END SCF
&XC
&XC_FUNCTIONAL LDA
&END XC_FUNCTIONAL
&END XC
&END DFT
&STRESS_TENSOR
NDIGITS 4
&END STRESS_TENSOR
&END PRINT
&SUBSYS
&CELL
ABC 26.0369999999999990 9.1050000000000004 6.2900000000000000
MULTIPLE_UNIT_CELL 1 1 1
SYMMETRY ORTHORHOMBIC
&END CELL
&COORD
Mg -8.5841870397562470E-02 2.4446737869627219E-01 4.8382391457694479E-01
Mg 2.6031406086949271E-01 2.6092719343831572E-01 4.4217146672191654E-01
Mg 5.8328369689563009E-01 2.7457651320156096E-01 5.4373784721259688E-01
Mg -1.6551265244923527E-01 5.0062949446903793E-01 4.1425269983661733E-01
Mg 1.7504514944695440E-01 4.8334791029082946E-01 5.1221241800498718E-01
Mg 5.0100847251823832E-01 5.1467931925712862E-01 5.3871665439449057E-01
Mg 4.9696258783467661E-03 2.8564556687435058E-02 -5.5635394771647945E-02
Mg 3.3341069514857558E-01 4.3041475940459976E-02 7.2042674649568979E-03
Mg 6.6442011772974674E-01 7.8685228117939057E-02 -1.2914007205212010E-02
Mg -8.8965855464970933E-02 3.0757986909734858E-01 -1.7341304196210550E-02
Mg 2.6429480997107940E-01 2.9871264106622647E-01 -1.1588724444114285E-04
Mg 5.9663827162760652E-01 3.2436772679716008E-01 1.4053134928836836E-03
Mg 8.3963502182136829E-02 2.2560437235288969E-01 4.5755778075376385E-01
Mg 4.1680405569713747E-01 2.5279272185825119E-01 5.1166415618287830E-01
Mg 7.5782180365131513E-01 2.5740119746015044E-01 5.0321085850400704E-01
Mg 1.0012635472290692E-02 4.9177815625580329E-01 5.0542111791271982E-01
Mg 3.4826208963496036E-01 4.9244069485338821E-01 5.3543844342620606E-01
Mg 6.7617022771933921E-01 4.9093655765936467E-01 4.3813890750518381E-01
Mg -1.7218244414747880E-01 5.5919241943238295E-02 -3.0553492021523139E-02
Mg 1.7385353536448078E-01 8.1253409311228611E-03 5.9398609267433799E-03
Mg 5.0334906666302892E-01 4.1457643446633649E-02 3.8409145603852696E-02
Mg 9.0018318897402805E-02 3.0490848749171917E-01 2.4777148653723682E-02
Mg 4.2759112826818119E-01 3.3550241386878465E-01 2.3574288059742265E-02
Mg 7.6029010663652807E-01 3.1034820319365952E-01 -7.7023048895912327E-02
Mg -8.1313873877322862E-02 7.7313009491039986E-01 4.3461633154845569E-01
Mg 2.4331569943035028E-01 7.3221060103160474E-01 5.1839726066449121E-01
Mg 5.9219372315569052E-01 7.2690449382934397E-01 4.9708940180974087E-01
Mg -1.5023352778399374E-01 9.9804254663294489E-01 4.6895512817445412E-01
Mg 1.7747341524146643E-01 9.8395743227503896E-01 5.3463993730437831E-01
Mg 5.0519021038414380E-01 1.0007092110747235E+00 5.0046645715607063E-01
Mg -2.2470938063514673E-03 5.5717466274186511E-01 -2.4260363411724203E-02
Mg 3.3247183757664761E-01 5.7859926774950377E-01 -1.8963323628777000E-02
Mg 6.6710460915604308E-01 5.4711297978742368E-01 -1.8744795300869112E-02
Mg -6.9702901123363123E-02 8.1471277075959991E-01 -1.3694208100214843E-02
Mg 2.5266844568200930E-01 8.1442337341414928E-01 -3.0440293716887004E-03
Mg 5.9155869762889146E-01 8.0276564100592418E-01 2.8292242575817007E-03
Mg 8.5198439961117159E-02 7.2502463201591161E-01 4.7741023096073743E-01
Mg 4.2797150764181374E-01 7.3183873081787887E-01 5.7055317612785195E-01
Mg 7.4627180458684039E-01 7.6710443821753282E-01 4.9709870301145453E-01
Mg -5.8810617600903881E-03 9.9267467333396797E-01 4.5006985665657040E-01
Mg 3.4547972080063727E-01 9.7433640024046786E-01 5.2063541360370935E-01
Mg 6.7069899018667600E-01 9.8999935891476076E-01 4.6416642311786444E-01
Mg 1.6619195913826168E-01 5.6494493718312333E-01 1.8350295635919005E-03
Mg 5.1023411830493037E-01 5.5831351058750600E-01 -3.8267644482570563E-02
Mg 8.3634339585256257E-01 5.5467337454304844E-01 7.8009284329952728E-03
Mg 8.4720040699066204E-02 7.7745794948872027E-01 -2.1561455207449107E-02
Mg 4.3489025913152479E-01 8.3641628928970846E-01 1.9941806566879525E-02
Mg 7.5419086823247095E-01 7.7190236576453275E-01 -2.5980926763719558E-02
Si -1.6728356246780929E-01 2.8232272664060165E-01 2.1558479386125443E-01
Si 1.7791388760609078E-01 2.7698111204688136E-01 2.7041876731432823E-01
Si 5.1440565600981436E-01 3.1896093411827270E-01 2.0620776655304177E-01
Si -7.5382514071711884E-02 4.1774027816088320E-02 2.0219155003479139E-01
Si 2.5642494482412936E-01 1.7623959610342122E-02 2.4932156137609984E-01
Si 5.8382910456387771E-01 2.9871433525202728E-02 2.4972175621105297E-01
Si -7.7283222438805949E-02 1.0036040156320534E+00 -2.8302178874664957E-01
Si 2.5899578237135035E-01 1.0285787167602245E+00 -2.7687563656782110E-01
Si 5.9156815965151488E-01 1.0223842301915391E+00 -2.6162822205629216E-01
Si -1.6517454406786483E-01 2.5635298362814551E-01 -2.6994044392031807E-01
Si 1.7939776418951683E-01 2.8464306969936548E-01 -2.5399808353232317E-01
Si 5.0542957339013084E-01 2.7111377918624624E-01 -2.9980422429052739E-01
Si 2.0323415780992295E-03 2.7779541789661716E-01 2.4671233314957591E-01
Si 3.4103948579684734E-01 2.6421176739814001E-01 2.5298110434427307E-01
Si 6.8278819590801654E-01 2.7528119667098000E-01 2.1297589505608711E-01
Si 8.5455304988850622E-02 1.0201354135682468E+00 2.4360345980615253E-01
Si 4.2441886884211777E-01 1.0582001614595029E+00 2.4545414981522820E-01
Si 7.6284723598227533E-01 1.0246937028042182E+00 2.3573758092393254E-01
Si 9.0434407921566901E-02 1.2080918715200891E-02 -2.5561808444944212E-01
Si 4.2539570597791759E-01 1.6024835047054074E-02 -2.4129761989223139E-01
Si 7.5361681011693626E-01 1.7345499591522894E-02 -2.4183432340715560E-01
Si 4.0214016112855768E-03 2.6733818264111503E-01 -2.5736571860243879E-01
Si 3.4325827442590690E-01 2.3718624650465039E-01 -2.5233475548346285E-01
Si 6.7377368672748161E-01 2.6802314483608120E-01 -2.8770164636283735E-01
Si -1.6438486662668073E-01 7.7925008023812892E-01 2.2749162278489696E-01
Si 1.6935052292611530E-01 7.6421962754004247E-01 2.5746508918875061E-01
Si 5.1195248976614460E-01 7.7270469269255471E-01 2.8921649405910033E-01
Si -8.1292853372605861E-02 5.2258636422540261E-01 2.1334993297416041E-01
Si 2.5586956978520836E-01 5.2541193405891462E-01 2.3064885447020086E-01
Si 5.9907922064845587E-01 5.2492735678963398E-01 2.3917225394417080E-01
Si -8.4039745698287482E-02 5.0821587002063040E-01 7.0708706469043636E-01
Si 2.5973751241889526E-01 5.2773505997819559E-01 7.5485919505089094E-01
Si 5.9026490822014377E-01 5.2198923213626380E-01 7.5916217382059015E-01
Si -1.6161104078241190E-01 7.5795256913335007E-01 7.1615013879434641E-01
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SCALED T
&END COORD
&TOPOLOGY
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY
&KIND Mg
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q10
&END KIND
&KIND Si
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q6
&END KIND
&CELL
&END CELL
&KINDS
BASIS_SET
POTENTIAL
&END KINDS
&END PRINT
&END SUBSYS
&END FORCE_EVAL
initial coordinates (head of pos file) of the initial model
240
i = 0, time = 0.000, E = -5533.8818888693
Mg -2.2350647795 2.2258754830 3.0432524227
Mg 6.7777972029 2.3757420963 2.7812585257
Mg 15.1869576161 2.5000191527 3.4201110590
Mg -4.3094529318 4.5582315471 2.6056494820
Mg 4.5576505562 4.4008827232 3.2218161093
Mg 13.0447575990 4.6861552018 3.3885277561
Mg 0.1293941490 0.2600802886 -0.3499466331
Mg 8.6810142696 0.3918926384 0.0453148424
Mg 17.2995066053 0.7164290020 -0.0812291053
Mg -2.3164039787 2.8005147081 -0.1090768034
Mg 6.8814439672 2.7197785969 -0.0007289308
Mg 15.5346706784 2.9533681525 0.0088394219
Mg 2.1861577063 2.0541278103 2.8780384409
Mg 10.8523271982 2.3016777325 3.2183675424
Mg 19.7314063017 2.3436379029 3.1651963000
Mg 0.2606989898 4.4776401127 3.1790988317
Mg 9.0677000278 4.4836725266 3.3679078092
Mg 17.6054442191 4.4699773575 2.7558937282
Mg -4.4831142983 0.5091446979 -0.1921814648
coordinates after 20ps
240
i = 20001, time = 20001.000, E = -5534.1383369278
Mg -8.5212228136 -17.2329853845 -6.1595394457
Mg 0.1733030533 -17.2261286967 -6.2821580924
Mg 8.9959146485 -17.4095596792 -6.3696605785
Mg -10.5729449901 -14.6903815393 -5.8709632264
Mg -1.6408954749 -14.7889119922 -6.1154406061
Mg 7.0096825252 -15.0695676381 -6.2952011201
Mg -6.5462144938 -18.6352030196 -9.2394688534
Mg 2.7079580192 -19.2117381190 -9.0573553409
Mg 11.0703485543 -19.0039397574 -9.3380730778
Mg -8.2970565765 -16.4689058371 -9.2340818459
Mg 0.4952232634 -16.9586463739 -9.4256184855
Mg 9.2344598716 -16.8880682175 -9.2526558096
Mg -4.2037103591 -17.0867382294 -6.0038126867
Mg 4.9376923386 -16.7217767801 -6.2864741981
Mg 13.1878255020 -17.2638944927 -6.2403029009
Mg -6.0381312891 -14.7081735538 -6.3737176302
Mg 2.3822045804 -14.6944383387 -6.1485179972
Mg 11.4396035728 -14.8853543043 -6.3185200850
Mg -10.4231395906 -18.8180442052 -9.3533964840
Mg -2.0886701394 -18.8927968592 -9.5809690521
Mg 6.8530648011 -18.8965492739 -9.4719921566
Mg -4.0205717577 -16.5417084935 -9.1752344616
Mg 4.7672752630 -16.7706042565 -9.2988751763
Mg 13.2134011273 -16.7797712709 -9.4822572983
Mg -8.3513203967 -12.4424046604 -6.3338283428
Mg 0.1740399213 -12.6675128344 -6.0703348080
Mg 9.1188169422 -12.9013949048 -6.1136900038
Mg -10.3195768248 -10.1868043404 -6.1259349808
coordinates after 70ps
240
i = 75001, time = 75001.000, E = -5534.1134699400
Mg -29.9516376336 -15.1194881940 -105.6864548489
Mg -21.4511789621 -15.2926359800 -106.1107492361
Mg -12.3363043787 -15.5007476138 -106.2108320349
Mg -32.2417730367 -12.9827426855 -105.5340500595
Mg -23.4138501483 -12.4400416991 -106.1547836826
Mg -14.7562896521 -13.1941836426 -106.0632110738
Mg -27.8160910483 -16.6746036456 -109.2618664112
Mg -19.3826628235 -17.1830156386 -109.1795648209
Mg -10.5844317056 -16.9004665903 -109.1913904136
Mg -29.8214023359 -14.3215323946 -109.1082157156
Mg -21.3262188298 -14.6000591188 -109.3459316789
Mg -12.5883003718 -14.7171299129 -108.9683410866
Mg -25.8265527209 -14.9827801002 -106.1365938986
Mg -17.1148136255 -15.5361901256 -105.8236732361
Mg -8.4142552222 -15.0898366321 -106.0625881355
Mg -27.5560141815 -12.8040524795 -105.9702759551
Mg -19.0600590386 -13.1822114701 -105.8094803560
Mg -10.3985974837 -12.9584366337 -106.0224361393
Mg -32.3640441320 -16.7883161725 -108.8004958341
Mg -23.7100783179 -16.5857359895 -109.1708486711
Mg -14.7782068474 -17.3885317222 -109.0902597143
Mg -25.3286013327 -14.4648690199 -109.0576491752
Mg -16.8045905059 -15.0924280776 -109.2360875952
Mg -8.0511065290 -14.4302778422 -108.8879246410
Mg -30.0144113017 -10.4071856423 -105.7877594307
Mg -21.3870390974 -10.6425949879 -106.0301613661
Mg -12.5339204264 -10.8533353879 -105.9856478294
Message has been deleted
Conrad
Jan 30, 2016, 5:02:00 AM1/30/16
to cp2k
Dear Tau Liu,
You should always post the information specified at: https://www.cp2k.org/howto:gethelp
Without it, it will be very difficult for users to help you!
Best wishes,
Conrad
Conrad Johnston
Queen's University Belfast
tao liu
Feb 1, 2016, 1:41:30 AM2/1/16
to cp2k
Hi Conrad,
I have added some extra information. Thanks
Regards,
Tao
I have added some extra information. Thanks
Regards,
Tao
Samuel Andermatt
Feb 1, 2016, 9:06:36 AM2/1/16
to cp...@googlegroups.com
I don't think there is such a keyword. You probably need to use a script to parse the data and apply the periodic boundary conditions.
Best
Samuel
Best
Samuel
tao liu
Feb 2, 2016, 1:39:12 AM2/2/16
to cp2k
Hi Samuel,
Thanks for your reply.
Yes it is easy to do that by a script with just several lines.
Regards,
Tao
Thanks for your reply.
Yes it is easy to do that by a script with just several lines.
Regards,
Tao
tao liu
Feb 3, 2016, 5:46:07 AM2/3/16
to cp2k
Hi All,
I found this keyword &CENTER_COORDINATES could center the atoms almost in the box without changing anything else.
Regards,
Tao
I found this keyword &CENTER_COORDINATES could center the atoms almost in the box without changing anything else.
Regards,
Tao
tao liu
Feb 9, 2016, 4:38:42 AM2/9/16
to cp2k
Hi All,
I have tested the keyword &CENTER_COORDINATES, but this keyword just works for the first step, CP2k will center all the atoms to the default position cell/2.. But in the following steps, the center of atoms will change along with simulation time. Do I understand correctly? If yes, is there anyway to carry out this &CENTER_COORDINATES keyword in every timestep? Thanks.
Tao
I have tested the keyword &CENTER_COORDINATES, but this keyword just works for the first step, CP2k will center all the atoms to the default position cell/2.. But in the following steps, the center of atoms will change along with simulation time. Do I understand correctly? If yes, is there anyway to carry out this &CENTER_COORDINATES keyword in every timestep? Thanks.
Tao
Samuel Andermatt
Feb 9, 2016, 5:04:30 AM2/9/16
to cp2k
I don't think centering the coordinates is what you need, since this would not apply periodic boundary conditions. If the distance between atoms is larger than the unit cell, they would still be placed outside.
Matt W
Feb 9, 2016, 5:06:40 AM2/9/16
to cp2k
Hi Tao,
The keyword COMVEL_TOL in MD section will allow you to remove center of mass motion.
However, if it is drifting very far it probably indicates that your setup is not quite good enough in conserving energy/momentum etc.
If particles are just diffusing out of the central periodic image, this is not a problem, as you note above. You, or VMD or whatever visualizer you use, can just wrap them back.
Remember, in CP2K a nice thing is you can run a quick classical calculation to check how it handles COM motion etc with a nicely conserving setup, rather than waiting for a DFT run to finish.
Matt
mh H
Oct 13, 2019, 11:35:36 PM10/13/19
to cp2k
If we don't set COMVEL_TOL, results become wrong?
...
mh H
Oct 13, 2019, 11:40:13 PM10/13/19
to cp2k
without considering COMVEL_TOL in MD section, calculation is wrong?
Matt W
Oct 14, 2019, 2:59:08 PM10/14/19
to cp2k
No. But if there are no external fields then the centre of mass motion should be zero.
If it is not (and it won't be) there are some numerical errors. You need to decide what level of inaccuracy is OK for your simulation.
mh H
Oct 14, 2019, 11:12:55 PM10/14/19
to cp...@googlegroups.com
Thank you, dear Dr. Matt W, How about a system including a water droplet in a big box? we must consider COMVEL_TOL? because in this condition(NVT, BOMD) we have deformation and therefore moving the center of mass.
BEST
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