[CP2K:4779] Re: Semiempirical Geometry Optimization calculation with periodic boundary condition

Bharat Sharma bharats... at gmail.com
Thu Nov 7 19:38:32 CET 2013


Hello David,

Thank you for your suggestions. I will try. Here is my complete INPUT with
coordinates.

Thank you.

Bharat

*********************************************************
&FORCE_EVAL
  METHOD Quickstep
  &DFT
   CHARGE 0
   UKS T
    &QS
      METHOD AM1
      &SE
      &END SE
    &END QS
    &SCF
      SCF_GUESS ATOMIC
    &END SCF
  &END DFT
  &SUBSYS
    &CELL
      ABC 12.42 12.42 12.42
      PERIODIC XYZ
    &END CELL
    &COORD
  O         3.8230943318       -4.5198948649        5.2582488668
  H         4.4117593821       -5.4463322402        6.0596860669
  H         3.4089112739       -4.3176289104        6.4149806247
  O        -3.5612056858        1.8633025312        4.1469785659
  H        -3.3823543540        0.6906309631        4.4224847660
  H        -3.4885955188        2.0946812564        5.3996183543
  O         4.7086948517        3.0093829507        5.5464511841
  H         3.4262158642        3.4253180971        5.4782028172
  H         4.4579128961        2.5841332560        4.0875459268
  O        -2.7045923244       -0.2102004489       -3.5420257152
  H        -1.9939093671        0.4901891677       -2.6434576509
  H        -1.6770767416       -0.8062198960       -3.8915363498
  O        -3.6216543968        4.7004584483        5.7565880477
  H        -4.8833823363        4.8251865842        5.8114967791
  H        -3.9447391516        4.6873989245        4.4858624201
  O         5.3421447081       -0.1217505313        2.3239281663
  H         6.3886685734       -0.5183444773        2.8431670261
  H         6.2956040964        0.7869438015        1.9798473892
  O         4.1596195298       -5.7536764673       -0.2321266367
  H         3.0364542503       -5.4113326871        0.3505072545
  H         3.8249932555       -4.7905788631       -1.1998930336
  O        -2.7677897367       -3.4362924990       -1.2237401267
  H        -3.0571228916       -2.2194319904       -1.8147172497
  H        -2.0936433688       -2.4089247165       -0.6039159980
  O         5.7326722939       -3.1420476877        3.1441398518
  H         4.4891144628       -3.1901078429        3.5256475925
  H         5.0077941888       -3.0691162469        2.0818914121
  O         1.8655927568        4.0018105285        5.6091613765
  H         1.6481294638        2.7815183286        5.7207957003
  H         1.9231894440        3.9394825623        6.8720670966
  O         4.1375052157       -4.1169889939       -3.0371524865
  H         2.9170329830       -3.7327190948       -3.6019884434
  H         4.4913764104       -2.7576576960       -2.6754176093
  O         1.9871654379       -1.7808562073        1.0132132857
  H         1.4956276767       -2.4016243012        1.9335445590
  H         1.7274141884       -2.0552735562       -0.0686962102
  O         0.6513325188       -5.7978739003       -4.7563067307
  H         1.7949082911       -6.2902958474       -4.8694750267
  H         0.4252927215       -5.7724103191       -6.1363048623
  O         4.9831165787        3.9049035266       -3.4623226377
  H         4.5251075625        2.7865839706       -3.1950850168
  H         5.2621534715        3.8351355152       -2.2067690949
  O         2.8343986251       -1.7265674941        5.0957018393
  H         3.8901917364       -2.1104141142        5.6756518968
  H         3.2521343809       -0.6334705960        4.6349747217
  O        -0.1479206385        1.9981716633        5.9116582713
  H         0.1422339976        0.8030977940        6.1578598984
  H        -0.0864235441        1.7386060492        4.6196599471
  O         1.2272551990       -3.0117695026        3.4523637307
  H         2.0783696915       -2.5961838818        4.3674958664
  H         1.0660132084       -4.0130496587        4.2664825333
  O        -2.5397248533        2.8806483799        2.0741109075
  H        -1.5098655941        2.2599706114        2.2589599419
  H        -2.6209631153        2.6946708819        3.2721332728
  O         0.6738899383       -0.6128060815       -5.6128026799
  H         1.7202403738       -0.8676291902       -6.3604735082
  H         1.4302320591       -0.5183677872       -4.5721651977
  O        -1.2753495181       -0.8673605398        0.1044321785
  H        -1.2223619399        0.3974601211       -0.0527350062
  H        -1.0144907302       -0.7791400986        1.3121236061
  O        -3.9571563578        3.1480835597       -3.0975427170
  H        -4.2080297976        4.4192573404       -3.1385984521
  H        -2.8570588583        3.7128862665       -3.1985251337
  O         5.1859100090        4.4800678666        2.1984827712
  H         4.4013978525        3.6881982415        1.3959385690
  H         4.1130998223        5.1534828329        2.6583198701
  O         4.1854609441        1.2393397940       -3.0854099930
  H         4.8184865712        0.8510213936       -4.2248788205
  H         4.4096483092        0.0421519641       -2.6105001389
  O        -4.9447204667        5.9384731949       -2.7966460519
  H        -5.4472177991        6.5314233234       -1.7816421359
  H        -6.0926128191        6.4385014826       -3.1472691900
  O         5.0297403238       -2.3455559345        0.5702079817
  H         5.3511690005       -1.2931260170        1.3181707304
  H         3.5422535190       -2.0532842005        0.7433884076
  O         1.8945371353        1.0957984297        1.7508553995
  H         3.0381214506        1.4329047552        1.3208879374
  H         2.1961106991       -0.1311690464        1.1933286407
  O        -5.5733698128       -5.0902387913       -0.3758861288
  H        -6.7041675030       -5.3442819612       -0.0740418294
  H        -5.9938383703       -3.9336998317       -0.5704589087
  O        -4.7278846581        4.7949699714        2.7855690867
  H        -6.0114205857        4.7509272423        2.5392932894
  H        -4.7167766151        3.5028746336        2.2913331297
  O         5.3279775793        0.6992201889       -5.5706417256
  H         6.4511479381        1.1765754344       -5.4352792743
  H         5.4008580313        1.6004173063       -6.3629147992
  O         0.8727740244       -1.7432658898       -1.2923943573
  H         0.3010790073       -2.8472258063       -1.6988076221
  H        -0.2312850960       -1.6202825726       -0.9366604220
  O         3.7609385121        2.5391347684        0.3450413833
  H         4.9680346520        2.8111829643       -0.4882643248
  H         3.1897630072        3.3926450321       -0.5119973793
  O        -1.0649776727       -1.2464857344        2.9638278887
  H        -0.2662866134       -2.2400625291        3.0959394170
  H        -2.0135723256       -1.8278612038        3.1254280051
  O         2.1170545031       -5.5419702172        1.2919514207
  H         1.0652550305       -6.0955245369        1.1380415200
  H         2.6502653892       -6.0715573210        2.2797572146
  O        -0.6513987669       -3.5783155169       -2.9718593782
  H        -1.7277174488       -4.0936767941       -2.3447919780
  H        -0.0470593646       -4.8344690552       -3.1855804540
  O        -5.4663654588        2.1677032262        1.5863235537
  H        -4.1741193232        1.8958277158        1.8709523739
  H        -5.1789879857        1.8119220894        0.3533003666
  O         2.1170555880       -3.4111546528       -5.3519595376
  H         1.2448042154       -4.2708608193       -4.8375544944
  H         1.5313281141       -2.3789870678       -5.4479503673
  O        -1.2622635000        3.6406646822       -3.2684201995
  H        -0.9201859484        4.2430093332       -4.6325699442
  H        -0.8527584070        4.9261011387       -2.8346591715
  O        -5.3130145771       -4.9085599129        4.5436909515
  H        -6.3993891551       -4.4666875233        4.0177638092
  H        -4.8221097928       -5.3385790504        3.2854237959
  O         2.8243576869        5.7420587632        3.5093813753
  H         3.4475357352        6.5754870329        4.2995477798
  H         2.6227959313        5.1161303531        4.5954154470
  O        -4.1917296707        1.3570064133       -5.3818910995
  H        -3.4278543842        0.9236461294       -4.5147705972
  H        -3.9229377409        2.4070081331       -4.5758684708
  O         3.5258010318        0.8383199111        4.2631475877
  H         2.7296826381        0.6907149867        3.1933008167
  H         4.3836547868       -0.0095241513        3.5390456395
  O        -4.5025690356       -0.7557459026        3.9354780593
  H        -5.3535292154       -1.4061913692        4.7062150294
  H        -4.2451336382       -1.9946125810        3.8500291124
  O        -0.4380654439        1.4390700425        3.1940423464
  H         0.6811252395        1.5058735601        2.6051605347
  H        -0.2592668167        0.1778218376        3.1576033675
  O        -1.9149706811        5.0900162910        0.4377449270
  H        -2.4223869635        4.0255635368        0.9899205117
  H        -2.5958133388        5.9525704817        1.0582087947
  O        -1.6256152064       -1.9580160385       -4.8956854261
  H        -0.4695093212       -2.3465714100       -4.3524809611
  H        -0.5339384492       -1.3086116820       -5.5246608862
  O        -5.0936835915        1.7522574988       -1.0713684229
  H        -4.8873921039        2.6748581414       -1.9895576687
  H        -5.5049370565        0.9526258996       -2.0772896905
  O         4.7822538107       -1.2717756755       -2.0872865313
  H         6.0945661610       -1.0719544575       -2.2139370457
  H         4.9082025622       -1.3564020380       -0.9122921692
  O        -0.6237849041        1.2386854086       -1.5381137773
  H        -0.7135342896        2.3303753598       -2.3219243091
  H         0.3172258322        0.9530112803       -2.2583936246
  O         0.1855806308        5.7703380995       -1.2658899442
  H        -0.1006795170        7.0279668765       -1.1306583500
  H        -0.9124231374        5.5846283801       -0.4996291954
  O         5.5359127346       -1.7857832652        5.7183116653
  H         6.2442680474       -2.3479676118        6.6132244823
  H         5.7193581804       -0.8592768797        6.8560328838
  O        -2.3722188766       -5.5675554953       -4.2183479483
  H        -2.4473443707       -6.8468293563       -4.5397236813
  H        -3.5392273884       -5.9010509485       -3.6919759280
  O        -5.0566656629       -1.2804952949       -3.1233232526
  H        -4.9578252937       -2.4424189805       -3.8437836216
  H        -3.9125179983       -0.8778083124       -3.3653093055
  O         2.4224926830        4.3124582854       -1.3098664930
  H         1.2497658249        4.3317602980       -1.0441246827
  H         2.5522650042        5.5249850912       -0.8611320513
  O        -5.7464780604       -3.7920156704       -5.0281968210
  H        -4.7650000054       -4.1243466295       -5.8797989835
  H        -6.4243495564       -4.6083956605       -5.9642399492
  O        -0.1809305646        5.1101453408        3.0090554933
  H        -0.7913900935        4.1570625107        3.5843672894
  H        -0.8773429285        4.7266812044        1.9472771533
  O        -2.9262978460       -3.9760589026       -6.3928557269
  H        -2.7508267626       -4.8734613988       -5.4631686351
  H        -2.1069579541       -3.1742462964       -5.8150905348
  O        -2.7839196045       -3.3452806415        3.5485724397
  H        -3.0074881941       -4.1845269137        4.4176725045
  H        -3.0999557455       -3.9315476706        2.5911848767
  O         2.3806062254        4.7398054413       -4.1381208167
  H         3.5130758683        4.5192007325       -3.6012586758
  H         1.9719332501        4.5198151860       -2.9804608713
  O         1.4450109296        0.2935787476       -3.1284579098
  H         1.7883538450       -0.7672155657       -2.6285197465
  H         2.6149551735        0.4677648699       -3.0598789725
  O        -0.9957515532        4.4986978562        6.0443757494
  H        -0.8631216686        3.0355913937        5.9592751927
  H        -2.2633009107        4.3536458576        5.8027402791
  O        -0.5144255324       -3.8966385064        0.2806810323
  H         0.4975005805       -4.0055251828        1.3089433825
  H        -1.2356001907       -4.4891030043        1.4358564378
  O         5.8036109755        5.7970313839        6.0042588118
  H         5.2413091025        4.6535298826        5.4779581385
  H         6.4462508991        6.2123485591        4.8260009215
  O        -0.1561553634       -5.1035308246        4.7274965740
  H        -0.6465244271       -6.3073794820        4.0619144434
  H        -1.4024382439       -4.8118220454        5.2205370964
  O        -3.6879351221       -5.2988773511        1.8854650848
  H        -4.3341877560       -6.3605752021        1.9637700336
  H        -4.4414028513       -5.4658411288        0.7926068865
    &END COORD
  &END SUBSYS
&END FORCE_EVAL
&MOTION
  &GEO_OPT
   MAX_ITER 5000
  &END GEO_OPT
&END MOTION
&GLOBAL
  PROJECT 64-water
  RUN_TYPE GEO_OPT
&END GLOBAL
*********************************************************


On Thu, Nov 7, 2013 at 1:33 PM, David Stelter <base... at gmail.com> wrote:

> Hi Bharat,
>
> You can simply supply more SCF iterations to try to force a convergence to
> solve your SCF problem. By default, MAX_SCF is 50 iterations with an
> accuracy (EPS_SCF) of 1x10^-5. These parameters can simply be added to your
> input file under the SCF section. Hopefully, the SCF convergence will fix
> the geometry problems! I am unable to test this for you as did not provide
> coordinates in the input file for your system.
>
> Best,
> David
>
>
> On Wednesday, November 6, 2013 11:13:26 AM UTC-5, bharat wrote:
>
>> Hello Everyone,
>>
>> I am trying to perform geometry optimization calculation using
>> semiempirical methods AM1, PM3, RM1, and PM6 with periodic boundary
>> condition for bulk water (64 water molecules, initial structure is from M.
>> D. Ben et al. J. Phys. Chem. Lett. 4, 3753 (2013)) . It is found that SCF
>> is not converged and the structures are very bad. (O-H bond lengths
>> increased to 5-8 A and structure is not converged.)
>>
>> Does anyone have experience using semiempirical methods for PBC
>> calculation? Please see the .xyz file using AM1 method.
>>
>> All suggestions are appreciated.
>>
>> Thank you.
>>
>> Bharat Sharma
>>
>>  --
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