6.6. geom with CP2K

Tip

CP2K is highly powerful for clusters in periodic systems, like surface-supported, or zeolite-absorbed systems. However, it is also highly complicated. You’d better have some experience of condensed-phase physics or solid quantum chemistry before reading this section.

To use CP2K with geom, you need two files: misc/runCP2K.sh and CP2K.tmp.

misc/runCP2K.sh is a script to call CP2K. There is ONLY 1 line that you need to change:

runCP2K.sh
1cp2kcmd="mpirun cp2k.popt"

You need to change it so you can correctly call CP2K on your hardware, like srun -n 192 cp2k.popt or /opt/cp2k-8.0/cp2k.popt.

CP2K.tmp is a CP2K input template. You’d better ONLY change the following parts:

CP2K.tmp
 1CHARGE       0
 2MULTIPLICITY 1
 3!     LSD
 4!     SURFACE_DIPOLE_CORRECTION T
 5!     SURF_DIP_DIR              Z
 6BASIS_SET_FILE_NAME    BASIS_MOLOPT
 7POTENTIAL_FILE_NAME    GTH_POTENTIALS
 8... omitted ...
 9PARAMETER_FILE_NAME  dftd3.dat
10... omitted ...
11&CELL
12   A                  30.00000000    0.00000000    0.00000000
13   B                   0.00000000   30.00000000    0.00000000
14   C                   0.00000000    0.00000000   30.00000000
15   PERIODIC            XYZ
16   MULTIPLE_UNIT_CELL  1 1 1
17&END CELL
18... omitted ...
19&KIND H
20   BASIS_SET DZVP-MOLOPT-SR-GTH
21   POTENTIAL GTH-PBE-q1
22&END KIND

To sum up, you need to change:

  • The CHARGE and MULTIPLICITY of the system.

  • If MULTIPLICITY is not 1, then LSD should be un-commented.

  • For surface-supported systems, un-comment SURFACE_DIPOLE_CORRECTION T and SURF_DIP_DIR Z. Please ensure that the vacuum direction should be Z.

  • The paths and filenames for BASIS_SET_FILE_NAME, POTENTIAL_FILE_NAME, and PARAMETER_FILE_NAME.

  • The cell constants A, B, and C.

  • The basis sets for each element, KIND.

  • If you understand exactly what you are doing, you can change anywhere.

6.6.1. Example: Graphene oxide-supported Cu8

Tip

The sample input and output files can be found in testfiles/geom/6-gocu8-cp2k.

Let’s see how 8 \(\text{Cu}\) are supported over the surface of a graphene oxide. The structure of the graphene oxide model is:

go.xyz
  1124
  2-829.3320055707
  3C         0.6432795582        1.4146381445       12.9802103805
  4C         1.8638405295        0.7068348736       13.1358213883
  5C         3.0803261454        1.4117958723       13.2926182146
  6C         4.2826452613        0.7049969815       13.4870725811
  7C         5.4908939226        1.4183747968       13.6173292256
  8C         6.6945610217        0.7086518738       13.7044774152
  9C         7.9024899763        1.4278111301       13.7202904813
 10C         9.1068015792        0.7190504163       13.6370502922
 11C        10.3144403340        1.4355578787       13.5249758495
 12C        11.5141472647        0.7292051997       13.3245409163
 13C        12.7285238514        1.4409268334       13.1735625500
 14C        13.9454351317        0.7326485987       12.9974247960
 15C        15.1770415433        1.4301435475       12.9268878534
 16C        16.4093490282        0.7204721712       12.9136194279
 17C         0.6527631899        2.8319555916       13.0403244189
 18C         1.8691198475        3.5247382130       13.2528534491
 19C         3.0871709142        2.8287137498       13.3671638582
 20C         4.2802068410        3.5288023773       13.6746472393
 21C         5.4929582858        2.8314678050       13.7365915100
 22C         6.6924957067        3.5357798292       13.9782707015
 23C         7.9043631825        2.8383988195       13.8719868403
 24C         9.1216246522        3.5404615840       13.9597571598
 25C        10.3210695315        2.8454166260       13.6974578387
 26C        11.5429395786        3.5450362446       13.6591436703
 27C        12.7356297186        2.8503322354       13.3275571037
 28C        13.9651113637        3.5501152720       13.2375295895
 29C        15.1851408619        2.8472003599       13.0203390970
 30C        16.4208344084        3.5359621542       13.0533771591
 31C         0.6441811503        5.6279654088       13.3965857081
 32C         1.8728741720        4.9242285617       13.4881166107
 33C         3.0318853880        5.5796320552       13.9222434798
 34C         4.2649866705        4.9134821550       14.0198081831
 35C         5.4335432648        5.5637056006       14.4877076867
 36C         6.6808855036        4.9105244991       14.3827642479
 37C         7.9080442650        5.5594291871       14.6773251573
 38C         9.1266636524        4.9126119226       14.3624572194
 39C        10.3842966168        5.5650364964       14.4594029340
 40C        11.5549663178        4.9229088327       14.0219032123
 41C        12.7947229064        5.6371718819       13.8807376941
 42C        13.9748547953        4.9457164036       13.4445846528
 43C        15.1953657892        5.6370386229       13.3406252865
 44C        16.4313478432        4.9426895690       13.2131835785
 45C         0.6543708202        7.0373885448       13.5438567265
 46C         1.8064599541        7.7182584078       13.9251444122
 47C         2.9229822840        6.9418844917       14.4259195724
 48C         4.0618007814        7.6106729179       15.0907651413
 49C         5.3621801507        6.8770322789       15.1711001143
 50C         6.6108186191        7.5877082532       15.5815224661
 51C         7.9279193292        6.8764197120       15.3683430735
 52C         9.2242243383        7.5935096830       15.5373883633
 53C        10.4876471939        6.8906080702       15.0962810702
 54C        11.7728595787        7.6409078920       14.9164998313
 55C        12.8462241580        7.0004281339       14.1357675067
 56C        14.0017035182        7.7276022730       13.7700768308
 57C        15.2040163359        7.0351375742       13.4515730393
 58C        16.4229251336        7.7300709199       13.4364821732
 59C         0.6397199388        9.8247108977       13.6732061241
 60C         1.8406768708        9.1253542496       14.0406383742
 61C         2.9135073628        9.8051709406       14.6150938055
 62C         4.0484428025        9.1048552407       15.2460375128
 63C         5.2987284042        9.8368977331       15.6301937214
 64C         6.6211748387        9.0957998585       15.8089307286
 65C         7.9318500618        9.8463453784       15.8249141248
 66C         9.2646748957        9.1015561413       15.7315438754
 67C        10.5397322088        9.8522535100       15.4656183286
 68C        11.8139498754        9.1289907885       15.0934109431
 69C        12.9303511297        9.8515482792       14.4466388818
 70C        14.0225893292        9.1129723112       13.8211288561
 71C        15.1994636428        9.8140577255       13.5375901623
 72C        16.4361778290        9.1248747195       13.4886746469
 73C         0.6156845872       11.2204744941       13.6336774460
 74C         1.7707140395       11.9395262563       13.9607604011
 75C         2.8382149430       11.2512379588       14.6910231987
 76C         4.1016042500       12.0523756371       15.0026016502
 77C         5.3556933694       11.3384053295       15.4384304526
 78C         6.6492978278       12.0529366184       15.2978289025
 79C         7.9567571765       11.3501665124       15.5603995693
 80C         9.2159999952       12.0650659421       15.1929597302
 81C        10.5355171840       11.3503696266       15.2060145604
 82C        11.6838859007       12.0119207895       14.5195180414
 83C        12.8397100557       11.2537212968       14.0976615062
 84C        13.9516390747       11.9070278478       13.6122930206
 85C        15.1878087576       11.2102445326       13.4681476887
 86C        16.3951276806       11.9083189243       13.4000184419
 87C         0.6163654218       14.0029006812       13.3725361122
 88C         1.8060481673       13.3152863013       13.7777899046
 89C         3.0337709241       14.0264152856       13.9533725170
 90C         4.2038561143       13.3762366275       14.3984184847
 91C         5.4666717537       14.0202351728       14.2922343720
 92C         6.6795574335       13.3731351172       14.6191869222
 93C         7.9122364175       14.0210216781       14.3493476581
 94C         9.1574077252       13.3680072124       14.4830244250
 95C        10.3314428153       14.0171847622       14.0234357387
 96C        11.5648907262       13.3500908525       13.9435509843
 97C        12.7232586488       14.0102079913       13.4929671042
 98C        13.9514266705       13.3146668780       13.3912841359
 99C        15.1581451102       14.0004348888       13.1796863119
100C        16.3991728698       13.3097718039       13.2847133689
101C         0.6249122629       15.4030054815       13.1827403520
102C         1.8539123277       16.0963334400       13.2730559211
103C         3.0498777826       15.4008132820       13.6015954952
104C         4.2750162180       16.0958512571       13.6456022309
105C         5.4732322826       15.3953324436       13.9015892724
106C         6.6920660341       16.0959266602       13.8341013562
107C         7.9025760729       15.3972335614       13.9518732463
108C         9.1045764348       16.1039358511       13.7355726252
109C        10.3156842660       15.4042212839       13.6785267189
110C        11.5080217157       16.1100041005       13.3819984075
111C        12.7231013720       15.4122132076       13.2570323075
112C        13.9366873102       16.1125499161       13.0382306452
113C        15.1674208815       15.4100047690       13.0259311494
114C        16.4018982276       16.1029067889       12.9865164230
115O         3.0685014966       11.8976422961       15.9914973499
116O         5.8997308342       12.0590412352       16.5628583623
117O         8.6648481614       12.1225614836       16.5532521702
118O        11.4887905099       12.0544944852       16.0159560496
119O         4.3325494195        9.4837710397       16.6372574825
120O         7.2474048771        9.4886444434       17.0444487372
121O        10.1426564634        9.4956180826       16.8066317309
122O        12.9071693327        9.5603206129       15.9270516525
123O         3.0611390859        6.9977122659       15.9237447506
124O         5.8373324975        6.8504468255       16.5552492288
125O         8.6593345773        6.8517129583       16.6396185079
126O        11.4886084289        6.9277293990       16.1522635888

The copper atom is:

cu.xyz
11
2Cu
3Cu 0 0 0

The input file is:

gocu8.inp
 1lm_dir          gocu8    # Save the local minima to this folder.
 2num_calcs       50       # Total number of calculations.
 3do_coarse_opt   yes      # no: Do NOT the coarse optimization.
 4min_energy_gap  1.E-4    # When two energies differ smaller than
 5                         # this value, they are treated as identical.
 6                         # A negative number means do not remove
 7                         # energetically degenerated ones.
 8max_geom_iters  3000     # The maximum number of iterations for local optimization.
 9                         # If it is less or equal than zero, then the number is unlimited.
10
11components
12    go.xyz 1
13    fix 0 0 0 0 0 0
14    ****
15    cu.xyz 8
16    random 0 0 2 7 7 4
17    ****
18end
19
20commands
21   ./runCP2K.sh $inp$ $out$ $xxx$
22end

In this input file, we fix the graphene oxide at (0, 0, 0) without rotations, and let the copper atoms distribute randomly over a part of graphene oxide.

We have also copied misc/CP2K.tmp and misc/runCP2K.sh to the current directory. The cell constants are set to:

CP2K.tmp
1SURFACE_DIPOLE_CORRECTION T
2SURF_DIP_DIR              Z
3... omitted ...
4A                  17.00000000    0.00000000    0.00000000
5B                   0.00000000   16.80000000    0.00000000
6C                   0.00000000    0.00000000   30.00000000

Note that we un-comment the surface options for this surface-supported cluster.

Now you can run the global optimization:

$ geom gocu8.inp > gocu8.out

After the optimization, the end of gocu8.out is

gocu8.out
 -- Result Report --
Results are energy-increasingly reordered.
Structures of energies within 1.000E-04 are treated as degenerate.
All minima are saved to "gocu8".
-------------------------------------------------------------------
     #  index               Energy            NaiveRMSD
-------------------------------------------------------------------
     0     24       -1214.21440464           0.00000000
     1      8       -1214.19223466           0.39353040
     2     17       -1214.17518232           0.67379764
     3     23       -1214.16671106           0.99591902
     4      7       -1214.15407074           0.93718398
     5     25       -1214.14564270           0.99740923
     6     12       -1214.14550906           0.83857957

Note that, in the first 4 clusters, the graphene surface are corrupted (some oxygen atoms dissociates from the surface) like gocu8/23.xyz. The true global minimum is gocu8/7.xyz. Both are shown below.

alternate text

6.6.2. Example: (H2S)5@SSZ-13

Tip

The sample input and output files can be found in testfiles/geom/7-h2s5ssz-cp2k.

We want to study the diffusion of \(\text{H}_2\text{S}\) in zeolite SSZ-13. The structure of SSZ-13 and \(\text{H}_2\text{S}\) are

ssz-13.xyz
  1108
  2SSZ-13
  3  O         5.7000232468        7.6303196339        2.6186286767
  4  O         5.2045498989       10.1995252965        3.2272552812
  5  O         7.6341828896        9.4099723840        2.7745789292
  6  O         5.8753034436        9.5497196844        0.7672162010
  7  O         7.6375473635        4.2759815544        2.6753670218
  8  O         9.5707533006        7.6299616532        2.6176480074
  9  O         9.6106668261        5.3414448452       13.6228779840
 10  O         7.6185326402        8.7535796994       13.6836873966
 11  O         5.6658146587        5.3461814248       13.6160993667
 12  O         5.7026893239       -0.2642085908        7.5407946669
 13  O         0.7825962064        8.1512328930        7.5378038833
 14  O         2.7836661828       11.6286830319        7.5359961843
 15  O         2.7363955771        9.3420684719        3.8535391861
 16  O         7.6423184053        0.8505970745        3.7730132707
 17  O        12.5335364638        9.3415768142        3.8544585628
 18  O        12.4624155643        3.6818551888       12.4626958554
 19  O         7.6062858624       12.1072824025       12.4587051589
 20  O         2.8065149113        3.6894351696       12.2320710199
 21  O         2.7322963802        1.4435907562        8.8508132419
 22  O         0.8127191930        4.8681935127        8.6967338458
 23  O        12.4822455137        1.3976417344        8.7679437480
 24  O         5.6527918209        2.5629377561        3.2319866240
 25  O        12.0423876809        6.7757052402        3.2233313473
 26  O        12.0554980341        6.2591391560       13.0723873245
 27  O         5.5916803863       10.4417381114       13.0790389503
 28  O         5.1667070765        2.7598543540       13.1500955201
 29  O        10.0234139879        2.7573797734       13.0802094325
 30  O         9.6173269693       10.4509455156       13.0839569435
 31  O         3.1861034312        6.1951039344       13.1391153838
 32  O         3.2262073712        6.7771124228        3.2237580685
 33  O         9.6209190582        2.5656089905        3.2277416465
 34  O        10.0640705757       10.1974856514        3.2288444611
 35  O         5.1427255382        2.3096527675        8.0673522413
 36  O        12.4246061731        6.5049032168        8.1596286214
 37  O         5.2287254916       10.6584161272        8.1499333643
 38  O        10.0660760251       10.7260767207        8.1486535093
 39  O         2.8490782073        6.5139838953        8.1476193260
 40  O        10.0374817601        2.3659377558        8.1472483774
 41  O         5.1316112190        5.0641064531        2.8432015310
 42  O        10.1446584873        5.0657040841        2.7757616149
 43  O        10.1029249905        7.9248177185       13.5271012901
 44  O         5.1139616931        7.9307810948       13.5327555244
 45  O         7.6221919820        3.6097600857       13.5295025529
 46  O         7.6288414056        1.5118665409        7.7615136197
 47  O        11.9654721427        9.0151964046        7.6848839357
 48  O         3.2451981211        9.0440458535        7.6881718795
 49  O         3.3069973094       11.9100887748        3.6976804332
 50  O         5.1307773743        0.0649280529        3.6340011283
 51  O         0.7969499830        7.5670851250        3.6935855226
 52  O         0.7910818700        5.3346368625       12.6820331150
 53  O        11.9636291062        1.1105277839       12.6111708865
 54  O         3.2392803629        1.1213561083       12.5479345449
 55  O         3.3075057508        4.0157430778        8.7760041016
 56  O        12.0156624591        3.9738388657        8.6139906116
 57  O         7.6320672727       11.5168215978        8.6125370060
 58  O         5.8866593170        3.4930627815        0.7891245303
 59  O        11.1355336190        6.5074683788        0.7610373808
 60  O         9.3801650379        3.4821683317        0.7717307825
 61  O         9.3883869933        9.5474036098        0.7666774122
 62  O         4.1692472661        6.4488991333        0.7780060769
 63  O         5.9556046254        1.6428018426        5.6765493427
 64  O        12.6861939240        7.3729754052        5.6887347990
 65  O         4.3586450055       10.4595476971        5.6921261702
 66  O         2.5801899718        7.3759353889        5.6905185401
 67  O         9.3400531831        1.7041165806        5.6889457138
 68  O        10.9432024258       10.5171940688        5.6851549584
 69  O        12.7365486472        5.5973335861       10.6155686479
 70  O         5.8478045129       11.3130579735       10.6124834850
 71  O         4.5150336200        2.4391618565       10.6065434296
 72  O         9.3801870229       11.2550644389       10.6124530044
 73  O         2.4362265224        5.7858392934       10.6232169362
 74  O        10.9023169714        2.5612785425       10.6093785249
 75 Si         6.0920814665        3.8508163034        2.3648358150
 76 Si        10.7202283849        6.5092425635        2.3328070616
 77 Si        10.7198656965        6.4925660943       13.9546031759
 78 Si         6.0652860896        9.1709124986       13.9647009255
 79 Si         6.0809445096        3.8112454238       13.9744263842
 80 Si         9.1680499571        3.8090892108       13.9600924915
 81 Si         9.1702883031        9.1714808622       13.9670464697
 82 Si         4.5450589507        6.4778439590       13.9665556825
 83 Si         4.5589301028        6.4970522597        2.3544741665
 84 Si         9.1776796571        3.8440220779        2.3459143784
 85 Si         9.1743108787        9.1858945424        2.3361918038
 86 Si         6.1023939667        1.2912554713        7.2563853198
 87 Si        12.8984444715        7.7609462493        7.2559239768
 88 Si         3.8937893347       10.4628352540        7.2542014120
 89 Si         3.8917972712       10.4639571217        4.1313484718
 90 Si         6.1021660505        1.2768708902        4.0983248150
 91 Si        12.9264443751        7.7793779850        4.1294213351
 92 Si         2.3418034349        7.7806749736        4.1302867232
 93 Si         9.1747023738        1.2939288098        4.1186514298
 94 Si        11.3852128233       10.4740999990        4.1168223128
 95 Si        11.3849847412       10.4645367999        7.2520286806
 96 Si         2.3463927644        7.7693527709        7.2545905923
 97 Si         9.1641901801        1.3288002236        7.2655864551
 98 Si        12.9252078158        5.2179055842       12.1892578243
 99 Si         6.0541114995       11.7025286295       12.1775311953
100 Si        12.9318493098        5.2383696707        9.0377621396
101 Si         6.0833435431       11.6953330771        9.0489768990
102 Si         9.1739017270       11.7144997047        9.0639602124
103 Si         2.3459232172        5.2847394268        9.0735577386
104 Si        11.3678806369        2.5575039972        9.0491343651
105 Si        11.3433313927        2.5385553857       12.1747149889
106 Si         9.1561829214       11.6952711342       12.1629072761
107 Si         2.3228901646        5.2436972032       12.1586452445
108 Si         6.0937069986        9.1867058586        2.3360857945
109 Si         3.9151902179        2.5466565165        9.0895664436
110 Si         3.9346333440        2.5195603195       12.1307588181
h2s.xyz
13
2H2S
3S                  0.00000000    0.00000000   -0.08403654
4H                  0.00000000   -1.06961052    0.67229231
5H                  0.00000000    1.06961052    0.67229231

The input file is:

h2s5-ssz-13.inp
 1lm_dir          h2s5-ssz-13 # Save the local minima to this folder.
 2num_calcs       50       # Total number of calculations.
 3do_coarse_opt   yes      # no: Do NOT the coarse optimization.
 4min_energy_gap  1.E-4    # When two energies differ smaller than
 5                         # this value, they are treated as identical.
 6                         # A negative number means do not remove
 7                         # energetically degenerated ones.
 8max_geom_iters  3000     # The maximum number of iterations for local optimization.
 9                         # If it is less or equal than zero, then the number is unlimited.
10
11components
12    ssz-13.xyz 1
13    fix 0 0 0 0 0 0
14    ****
15    h2s.xyz 5
16    random -2 -3 -4 2 3 4
17    ****
18end
19
20commands
21   ./runCP2K.sh $inp$ $out$ $xxx$
22end

In this input file, we fix SSZ-13 at (0, 0, 0) without rotations, and let \(\text{H}_2\text{S}\) distribute randomly in a box.

We have also copied misc/CP2K.tmp and misc/runCP2K.sh to the current directory. The cell constants are set to:

CP2K.tmp
1A                  13.67500000    0.00000000    0.00000000
2B                  -6.83750000   11.84289740    0.00000000
3C                   0.00000000    0.00000000   14.76700000

Now you can run the global optimization:

$ geom h2s5-ssz-13.inp > h2s5-ssz-13.out

After the optimization, the end of h2s5-ssz-13.out is

h2s5-ssz-13.out
 -- Result Report --
Results are energy-increasingly reordered.
Structures of energies within 1.000E-04 are treated as degenerate.
All minima are saved to "h2s5-ssz-13".
-------------------------------------------------------------------
     #  index               Energy            NaiveRMSD
-------------------------------------------------------------------
     0     27       -1358.80693816           0.00000000
     1      4       -1358.80673445           1.22396041
     2     48       -1358.80659506           1.24720115
     3     26       -1358.80633823           1.39830933
     4     30       -1358.80612440           1.21331541
     5     16       -1358.80600754           1.53879815
     6      5       -1358.80565466           1.06068612

So the global minimum is h2s5-ssz-13/27.xyz, which is shown below.

alternate text