[CP2K-user] [CP2K:16333] Re: PBC problem
kj43 tem
ktem395 at gmail.com
Fri Dec 3 09:44:22 UTC 2021
I realized that I put in the previous post, an input in which I had tried
to use POISSON_SOLVER IMPLICIT. Actually the results of the images are
obtained by putting POISSON_SOLVER ANALYTIC. I apologize for the mistake in
the previous post.
Il giorno venerdì 3 dicembre 2021 alle 10:39:57 UTC+1 kj43 tem ha scritto:
> Greetings, I have recently started using cp2k and I'm a beginner. I'm
> writing to you because I need help with a molecular dynamics calculation.
> My system consists of a silver surface that interacts with an aqueous
> solution. I applied the PBCs only along the X and Y axes, but not along Z
> (in that Z direction I have the solution that interacts with the surface).
> The silver surface is parallel to the XY plane I set in the & POISSON
> section:
> POISSON_SOLVER ANALYTIC Unfortunately, however, it happens that the bonds
> of some water molecules tend to break when they reach the edge of the
> simulation box along Z, as if the atoms interacted with the image of my
> surface, which is located along Z. I tried to change the algorithm to
> POISSON_SOLVER but got the same results. At this point, with the VMD
> software I entered the size of the simulation box that I entered in the
> Cp2k input and I visualized the system image along z. I observed (as you
> can see in the following image) that the hydrogen atoms tend to collapse
> towards the silver atoms of the image along z (this however should not
> happen because in PERIODIC I have set only the X and Y axes). These are the
> dimensions of the simulation box:
>
> &CELL ABC 16.36 16.36 16.78 PERIODIC XY &END CELL
>
> In the following images, however, we can see how the atoms that are
> subject to breaking of the bonds are "attracted" by atoms of the image
> surface along z (which should not exist, however).
>
> In the following image there is the initial situation:
> [image: 01.png]
>
> The following image shows the breaking of some chemical bonds: (this
> occurs after a few thousand of molecular dynamics steps)
> [image: 02.png]
>
> Finally, in this image I show the image of the system along Z, and it is
> evident that the hydrogen atoms converge towards a silver atom in the image: [image:
> 03.png]
>
> Here is my input: (I apologize for any mistakes but I am learning and I
> may have made many mistakes)
>
> &FORCE_EVAL
> METHOD QUICKSTEP
> &DFT
> &QS
> METHOD xTB
> &xTB
> &PARAMETER
> DISPERSION_PARAMETER_FILE dftd3.dat
> &END PARAMETER
> DO_EWALD T
> CHECK_ATOMIC_CHARGES F
> STO_NG 6
> &END xTB
> &END QS
> &POISSON
> PERIODIC XY
> POISSON_SOLVER IMPLICIT
> &EWALD
> EWALD_TYPE SPME
> &END EWALD
> &END POISSON
> &SCF
> SCF_GUESS ATOMIC
> MAX_SCF 250
> EPS_SCF 1.e-6
> &OT
> MINIMIZER CG
> PRECONDITIONER FULL_ALL
> ENERGY_GAP 0.01
> &END
> &OUTER_SCF
> EPS_SCF 1.e-6
> MAX_SCF 250
> &END
> &END SCF
> &END DFT
> &SUBSYS
> &CELL
> ABC 16.36 16.36 16.78
> PERIODIC XY
> &END CELL
> &COORD
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> O 1.1412196509336093E+01 3.3045544354346950E+00
> 1.3322890432595699E+01
> H 1.0456044896241609E+01 3.2509660240818290E+00
> 1.2984282915683531E+01
> H 5.6922076230432417E+00 1.4549687189353016E+01
> 9.9491785299095348E+00
> O 5.9513619554041135E+00 1.3677788558061962E+01
> 9.4806145746274915E+00
> H 5.0426730597894540E+00 1.3213427840578255E+01
> 9.4454972804446040E+00
> H 1.0200520080436204E+01 3.6794552488853713E+00
> 1.0418485639517936E+01
> O 1.0681274868473150E+01 2.7895518767831127E+00
> 1.0557399502052471E+01
> H 9.9013851566143760E+00 2.2083499481411151E+00
> 1.0863152457744642E+01
> H 1.4524156390317893E+01 3.1769265200677435E+00
> 1.2860771510300413E+01
> O 1.4238550228283700E+01 3.9482821334563720E+00
> 1.3458253439530873E+01
> H 1.3746454824348763E+01 4.5175798775635920E+00
> 1.2778114694504893E+01
> H 2.1260118810873223E+00 9.6284278552708233E+00
> 1.0560116835181045E+01
> O 1.7556909596308297E+00 8.7181084925571142E+00
> 1.0829763860113292E+01
> H 1.8319240246841064E+00 8.7505265285166729E+00
> 1.1852324703511302E+01
> H 1.6364833955513291E+01 1.9727680403444805E+00
> 1.0035503209535468E+01
> O 1.5759857684781050E+01 2.0215363551958578E+00
> 9.2203801813259680E+00
> H 1.5217488950575413E+01 2.8271399831139554E+00
> 9.5215763987236723E+00
> H 1.3228728285642424E+01 1.3226950602314810E+01
> 8.8214796375094338E+00
> O 1.4206991129407372E+01 1.3195346635350145E+01
> 8.5271991065372710E+00
> H 1.4622247918624671E+01 1.3171518143671749E+01
> 9.4620840518806801E+00
> H 1.9064000281673970E+00 1.7986661661929966E+00
> 1.0464450937799617E+01
> O 2.4207221158193515E+00 1.2999497051853295E+00
> 9.7440871214255367E+00
> H 2.2840714267025657E+00 1.9405388450345276E+00
> 8.9614395191594163E+00
> H 1.4729850319373933E+01 7.2240583491853547E+00
> 1.2870005844722844E+01
> O 1.5604954451986847E+01 7.4795701476372667E+00
> 1.3318172451713790E+01
> H 1.5343708112590601E+01 8.4139794024764782E+00
> 1.3633059798645865E+01
> H 3.0920873359504459E+00 1.2216982565563875E+01
> 1.2820969709667363E+01
> O 3.6508955731458990E+00 1.1798813960470126E+01
> 1.3560670360243666E+01
> H 4.4328028210761312E+00 1.2451443791694867E+01
> 1.3558077306523410E+01
> H 5.8931725130694295E+00 2.3542197530565105E+00
> 1.1383913800400542E+01
> O 5.3479445977486746E+00 1.5068068914867119E+00
> 1.1567103222891552E+01
> H 6.0019877633660270E+00 1.0010872273780460E+00
> 1.2183498135493732E+01
> H 4.4677894585142850E+00 3.3070190828460824E+00
> 1.1389544042333613E+01
> O 3.6160270912665942E+00 3.5522124395200021E+00
> 1.0877826337154373E+01
> H 2.8643527476465591E+00 3.3894505412477893E+00
> 1.1544488746210758E+01
> H 1.4868102365970959E+01 1.4263144711350465E+01
> 1.3520327276740714E+01
> O 1.4755774084349966E+01 1.3441725463114693E+01
> 1.4107731655718121E+01
> H 1.3864904478923654E+01 1.3096079072335552E+01
> 1.3751929353917012E+01
> H 4.5921964158251605E+00 9.0052699209715570E+00
> 1.1783525824484133E+01
> O 4.5282547207564381E+00 8.5194194938755370E+00
> 1.0890134509184859E+01
> H 3.7875674660982344E+00 7.8512211592038970E+00
> 1.1109266208980843E+01
> H 1.0036204899885425E+01 7.9489625620511957E+00
> 1.1653404210502284E+01
> O 1.0098371940973275E+01 6.9608896661342818E+00
> 1.1915347093183925E+01
> H 1.0547152864203712E+01 7.0491078016025801E+00
> 1.2832372726039928E+01
> H 1.4239530369935245E+01 9.7966074594622921E+00
> 1.2370235080981407E+01
> O 1.3898565895172695E+01 1.0731598334942175E+01
> 1.2601299656174007E+01
> H 1.3178864736408979E+01 1.0885312768349719E+01
> 1.1899052657185853E+01
> H 1.9753440892415941E-01 1.5364572490542821E+01
> 1.3343239766412506E+01
> O -1.6067736416028264E-01 1.6209706476890194E+01
> 1.2897855141542150E+01
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> 1.2802984099479998E+01
> H 2.9810178299678869E+00 5.5677174108156375E+00
> 1.3847950762717176E+01
> O 3.5369532301273550E+00 5.5170681356617450E+00
> 1.4697681945760886E+01
> H 3.5212591994670568E+00 4.5056806754361105E+00
> 1.4826105799320082E+01
> H 2.0268673689733419E+00 8.6525539760585541E+00
> 1.3066569117116334E+01
> O 1.5386593247211005E+00 9.0341028913446610E+00
> 1.3875950907832836E+01
> H 1.5799516914839689E+00 1.0010773984968671E+01
> 1.3577354459521475E+01
> H 5.0925105313403289E+00 3.4877065678820247E+00
> 1.3603225723228215E+01
> O 5.4402768212597001E+00 2.7753159199739841E+00
> 1.4239963379491586E+01
> H 5.1003329303167195E+00 1.9338758089077919E+00
> 1.3775373156258581E+01
> H 7.0392237580876404E+00 1.5349422619646393E+01
> 1.1814078012789283E+01
> O 7.5165786177333977E+00 1.5975885041869974E+01
> 1.1160611281364490E+01
> H 7.7184211737849315E+00 1.6802002517049647E+01
> 1.1738063301740633E+01
> H 6.7199560512257719E+00 1.1103379203558198E+01
> 1.3583074638850382E+01
> O 5.9640966550825807E+00 1.0423478675173754E+01
> 1.3597899721293990E+01
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> 1.4598627253205638E+01
> H 1.5615926846566840E+01 1.3783854657359383E+01
> 1.1806189450194138E+01
> O 1.5668459965991007E+01 1.2930531661638573E+01
> 1.1254690702966977E+01
> H 1.4735406644210322E+01 1.2538212744699701E+01
> 1.1352902406361935E+01
> H 7.9120997509787161E+00 1.1975320199371138E+01
> 9.4300184983318669E+00
> O 8.2253330303617584E+00 1.1024239630707465E+01
> 9.2199830207520286E+00
> H 9.2225129341524177E+00 1.1112574288624606E+01
> 9.4189702001640949E+00
> H 6.3088615258422900E+00 2.7665888371468665E+00
> 8.9104879763493940E+00
> O 5.5234421366731787E+00 3.4118795921807439E+00
> 8.9610593199490491E+00
> H 5.4933299746622302E+00 3.6780253463383081E+00
> 9.9458945994855714E+00
> H 4.0125369663215213E+00 5.4067508823041379E+00
> 9.7385073508415356E+00
> O 4.0221308878267275E+00 6.0181471290157900E+00
> 8.9220892476699731E+00
> H 3.2937867215421539E+00 6.6514861236917033E+00
> 9.2438099664571443E+00
> H 9.5157308121240760E+00 1.0412887010492064E+01
> 1.3766420559991396E+01
> O 8.8945655430272499E+00 9.6108776625002879E+00
> 1.3890450301473663E+01
> H 9.5090719972450799E+00 8.9227009007078166E+00
> 1.3464835968899083E+01
> H 9.0596685368937653E+00 1.3480797405054171E+01
> 1.5091150758091876E+01
> O 9.8789522191634518E+00 1.3397850226205906E+01
> 1.5699692621537427E+01
> H 1.0417678658528025E+01 1.2742786656088144E+01
> 1.5123242885329629E+01
> H 1.0121805117117521E+01 8.0167385314120363E+00
> 9.5472588364735511E+00
> O 1.0931393632054810E+01 8.5278713542123139E+00
> 9.1976917869625421E+00
> H 1.1457129560653859E+01 8.5509342483880992E+00
> 1.0074880939843327E+01
> H 4.4530148432660557E+00 1.5937293497748151E+01
> 1.3559784956077765E+01
> O 4.8067462210074048E+00 1.5760448989341985E+01
> 1.4495067818889769E+01
> H 5.4958579816188946E+00 1.6523357553128619E+01
> 1.4587358967930788E+01
> H 1.6243885823087844E+01 8.8717655563448936E+00
> 1.0523599139069795E+01
> O 1.5457047796812317E+01 9.1785298306708327E+00
> 9.9401225490329654E+00
> H 1.4809337329485567E+01 9.3707415105841410E+00
> 1.0704732691846674E+01
> H 7.9661510997408891E-01 4.3773427987910711E+00
> 9.4629111439899134E+00
> O 1.6436509957757610E+00 4.0942238673928921E+00
> 8.9741663337980775E+00
> H 2.2930348873580817E+00 4.6888775167748946E+00
> 9.5020252055895291E+00
> H 1.3183531937623528E+01 9.5131942067713613E+00
> 9.1271898176361574E+00
> O 1.3149463748202699E+01 1.0381086405440330E+01
> 8.5911176442091968E+00
> H 1.2543513849095907E+01 1.0921920925318432E+01
> 9.2007095882929164E+00
> H 1.2162678579194713E+01 1.5794073182145654E+01
> 9.1789262290251745E+00
> O 1.1840890394062809E+01 1.4918977062239364E+01
> 8.7655653900651735E+00
> H 1.0883635179343804E+01 1.4979074921619604E+01
> 9.1085324530542522E+00
> H 7.7594449510107841E+00 1.6387578447975066E+01
> 1.3503963548594026E+01
> O 8.3554837399856066E+00 1.6769298581739079E+01
> 1.4240356243336137E+01
> H 8.7185246808441033E+00 1.7570056813515325E+01
> 1.3719973773075733E+01
> H 9.1946774994007352E-01 1.4257911264440768E+01
> 1.1110065684189474E+01
> O 1.1119698356209684E+00 1.5064343941366049E+01
> 1.0523703147267394E+01
> H 1.8732718979447678E+00 1.5475425662405266E+01
> 1.1057291839875262E+01
> H 1.6620375906985321E+00 1.4031690162169635E+01
> 1.4036879950722744E+01
> O 1.1463233046508594E+00 1.3271484731406877E+01
> 1.4473085128526177E+01
> H 2.7202676858894437E-01 1.3359815117598238E+01
> 1.3955279432685499E+01
> H 9.0900554778134328E+00 1.4774713269925615E+01
> 8.7740096095609275E+00
> O 9.0841076204292399E+00 1.3782605843039011E+01
> 8.5615505590147301E+00
> H 8.6325013302621780E+00 1.3373141909038631E+01
> 9.3773088063033860E+00
> H 9.3352900737754201E+00 4.6649099715469440E+00
> 9.2160573708371381E+00
> O 9.8422694472223320E+00 5.1657640191980070E+00
> 8.4920224096670687E+00
> H 1.0271301004734129E+01 5.9031534533033989E+00
> 9.0512372752631940E+00
> H 1.1168470261784023E+01 1.1539970657550519E+01
> 8.9293600204422034E+00
> O 1.1366320330491366E+01 1.2504898179278223E+01
> 8.6766814039122515E+00
> H 1.0898612934696848E+01 1.2933615600868501E+01
> 9.4745790142430231E+00
> H 1.4196880053359250E+01 9.0881397662253693E+00
> 1.4583551212793159E+01
> O 1.3411436663574165E+01 8.5541062138736876E+00
> 1.4951070012622981E+01
> H 1.2679159979038538E+01 9.2623465194842733E+00
> 1.4894816831716074E+01
> H 1.2668363460340291E+01 1.8427803167493750E+00
> 1.0527576643438991E+01
> O 1.3372355027400440E+01 1.2374787112429926E+00
> 1.0101488761345378E+01
> H 1.3572107253811110E+01 6.9233124940455282E-01
> 1.0940490377404425E+01
> H 5.1444960172647853E+00 1.0707351163561595E+01
> 9.9239900082341403E+00
> O 4.8470442566945939E+00 1.1060672054714157E+01
> 9.0099907249200033E+00
> H 3.8742448053587335E+00 1.1246155099323110E+01
> 9.2679826383142139E+00
> H 1.1359681136803070E+01 1.4483316080393537E+01
> 1.4040814099325791E+01
> O 1.2146684346534171E+01 1.5132903875977728E+01
> 1.3960514790994377E+01
> H 1.2164656568601139E+01 1.5348594060017769E+01
> 1.2968857278528429E+01
> H 1.4279730864098395E+01 5.0093730736608357E+00
> 9.0823116602575773E+00
> O 1.3523515043812409E+01 4.4975484448310619E+00
> 8.6353788462984156E+00
> H 1.3519506410075280E+01 3.6798005409044512E+00
> 9.2415158472816259E+00
> H 1.7398913817627157E+00 4.7947646780744639E+00
> 1.3499274711809578E+01
> O 7.4843574393379997E-01 4.5972640875183233E+00
> 1.3381967710160596E+01
> H 7.8063506195760146E-01 3.8260047515146933E+00
> 1.2730406085580629E+01
> H 4.3601712699507473E+00 5.1000781397860466E+00
> 1.2258913534913582E+01
> O 4.7480663716290916E+00 6.0179138390533344E+00
> 1.2023282216713586E+01
> H 4.1303559809927455E+00 6.6166953778476527E+00
> 1.2576498268654630E+01
> H 5.5491865924931325E+00 5.0857518437164799E+00
> 1.4830996793528554E+01
> O 6.4722436575147402E+00 5.3874865761271824E+00
> 1.4509649200785335E+01
> H 6.4133333699033912E+00 5.0851010776979173E+00
> 1.3543315371372451E+01
> H 1.8373234805894856E+00 1.0759900055173981E+01
> 1.2020441837222492E+01
> O 1.4672223230327985E+00 1.1509785838563884E+01
> 1.1437029796595452E+01
> H 1.9571773542858768E+00 1.1364147150466755E+01
> 1.0557143639945940E+01
> H 1.3548159349007327E+00 6.5146018976766848E+00
> 8.9895027623555759E+00
> O 3.7403870674632939E-01 6.6823363893228098E+00
> 8.7743942729299942E+00
> H -3.5946164548139974E-02 5.8034469424041015E+00
> 9.0819048112506042E+00
> H 7.1107871694885096E+00 2.9957850379400530E+00
> 1.0395663198744657E+01
> O 7.8077085593728670E+00 2.3093730464430262E+00
> 1.0101639784280273E+01
> H 7.9043192449986526E+00 1.7695235559647979E+00
> 1.0966605596579099E+01
> &END COORD
> &END SUBSYS
> &END FORCE_EVAL
> &MOTION
> &CONSTRAINT
> &FIXED_ATOMS
> COMPONENTS_TO_FIX XYZ
> LIST 1..128
> &END FIXED_ATOMS
> &END CONSTRAINT
> &MD
> ENSEMBLE NVE
> STEPS 10000
> TIMESTEP 0.1
> TEMPERATURE 300.0
> TEMP_TOL 50.0
> &END MD
> &END MOTION
> &GLOBAL
> PROJECT testAg_surf
> RUN_TYPE MD
> PRINT_LEVEL LOW
> &END GLOBAL
>
>
>
>
>
> Thank you very much for your help.
>
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