User Tools

Site Tools


exercises:2017_ethz_mmm:c2h2_pdga

Adsorption of C2H2 on PdGa(111)

In this exercise you will compute the adsorption energy of acetylene on a intermetallic catalyst. This process is important during the production of polyethylene, and the system is described in this paper: 10.1021%2Fja505936b.

  • In the first part of the exercise you will consider the optimized configuration (already in the directory) and study the pure electronic adsorption energy, namely the difference between the total energy of the surface-molecule system and the energy of the molecule alone and surface alone in the same geometry as the surface-molecule system minimum structure. This will allow to show the binding pattern of the electronic density.
  • In the second part, you will optimize the surface and the molecule separately; this will allow to compute the total adsorption energy.

1. Task: Familiarize yourself

The coordinates of the optimized configuration are provided to you as S_M.opt.xyz (S stands for “Substrate”, M for “Molecule”, opt for “optimized”). Visualize the geometry with VMD and familiarize yourself with the system.

2. Task: Bond induced density differences

Compute the density difference induced by the adsorption bonding. For this you will have to run three separate energy calculations, using the *.ene.inp files.

  1. combined system (file S_M.opt.xyz)
  2. lone acetylene (file M.S_M.xyz)
  3. lone slab (file S.S_M.xyz)

In order to output the electronic densities as cube files, your input file has to contain the following snipped:

&DFT
  &PRINT
    &E_DENSITY_CUBE
    &END E_DENSITY_CUBE
  &END
&END DFT
The calculations involving the slab should be run on at least 16 cores with qsub run -v INP=prefix. Check the run file for the number of nodes.

To process the cube files we are going to use the cubecruncher tool. It is part of CP2K and is in your exercise directory.

you@eulerX ~$ ./cubecruncher.x -i S_M-ELECTRON_DENSITY-1_0.cube -subtract S-ELECTRON_DENSITY-1_0.cube -o tmp.cube
you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract M-ELECTRON_DENSITY-1_0.cube -o Delta_ads.cube

The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:

you@eulerX ~$ ./cubecruncher.x -center geo -i Delta_ads.cube -o Delta_ads-centered.cube

You can visualize the resulting file delta_ads-centered.cube with VMD. This has been covered in a previous exercise.

What you get should look similar to this:

3. Task: Bonding energies

Compute the binding energy:

\[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \]

For this you will need the energy values of three systems:

  1. lone acetylene molecule (run geometry optimization, use energy of last step)
  2. lone slab (you can use the already geometry optimized coordinates from S.opt.xyz at the end of the exercise)
  3. combined system adsorbed (can be reused from previous task)
You can not reuse the energy values for the lone sub-systems from the previous task. Since the unbound subsystems might relax into a different geometry, they have to be geometry optimized first.

Questions

  • Sketch briefly the geometry of the molecule when adsorbed and in the gas phase.
  • Report the system energy for the bonded system, lone slab, and lone molecule.
  • Can you estimate the contribution due to the geometry relaxation?
  • Briefly report the bond induced density difference on the system.

Required Files

When you are dealing with big systems and multiple atomic species, the input can be simplified by splitting it into multiple files. We are going to use separate files for the coordinates, the basis-sets, and the pseudo-potentials. All these files should reside in the same directory as the main input file.
The provided files are all in the directory /home/psd/Exercise_9. Change the name of the xyz file accordingly in the input files.
S_M.inp
&FORCE_EVAL
  METHOD Quickstep
  &DFT
  &PRINT
    &E_DENSITY_CUBE
    &END E_DENSITY_CUBE
  &END
    BASIS_SET_FILE_NAME ./BR
    POTENTIAL_FILE_NAME ./GR
    &QS
      EPS_DEFAULT 1.0E-10
      METHOD GPW
      EXTRAPOLATION ASPC
      EXTRAPOLATION_ORDER 3
    &END QS
    &MGRID
      CUTOFF 400
      NGRIDS 5
    &END
    &SCF
      MAX_SCF 20
      SCF_GUESS RESTART
      EPS_SCF 1.0E-5
      &OT
        PRECONDITIONER  FULL_SINGLE_INVERSE
        MINIMIZER  CG
      &END
      &OUTER_SCF
        MAX_SCF 50
        EPS_SCF 1.0E-5
      &END
      &PRINT
        &RESTART
          &EACH
            GEO_OPT 2
          &END
          ADD_LAST NUMERIC
          FILENAME RESTART
        &END
        &RESTART_HISTORY OFF
        &END
      &END
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
A [angstrom] 14.08557 0 0
B [angstrom] 0 12.1985 0
C [angstrom] 0.000000      0.000000    15.0
    &END CELL
    &TOPOLOGY
     COORD_FILE_NAME ./S_M.opt.xyz
     COORDINATE xyz
    &END
    &KIND Pd
      BASIS_SET DZVP-MOLOPT-SR-GTH-q18
      POTENTIAL GTH-PBE-q18
    &END KIND
    &KIND Ga
      BASIS_SET DZVP-MOLOPT-SR-GTH-q13
      POTENTIAL GTH-PBE-q13
    &END KIND
    &KIND C
      BASIS_SET TZV2P-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND H
      BASIS_SET TZV2P-MOLOPT-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PRINT_LEVEL LOW
  PROJECT S_M
  RUN_TYPE ENERGY
&END GLOBAL              

<!–

POTENTIALS
################################################################################
#
# Potential data base file for CP2K (Quickstep)
#
################################################################################
# -----------------------------------------------------
#
# Literature: - S. Goedecker, M. Teter, and J. Hutter,
#               Phys. Rev. B 54, 1703 (1996)
#             - C. Hartwigsen, S. Goedecker, and J. Hutter,
#               Phys. Rev. B 58, 3641 (1998)
#             - M. Krack,
#               Theor. Chem. Acc. 114, 145 (2005)
#
# Potential for the PBE functional
#
################################################################################
#
H GTH-PBE-q1
    1
     0.20000000    2    -4.17890044     0.72446331
    0
#
C GTH-PBE-q4
    2    2
     0.33847124    2    -8.80367398     1.33921085
    2
     0.30257575    1     9.62248665
     0.29150694    0
#
O GTH-PBE-q6
    2    4
     0.24455430    2   -16.66721480     2.48731132
    2
     0.22095592    1    18.33745811
     0.21133247    0
#
Ti GTH-PBE-q12
    4    6    2
     0.38000000    2     8.71144218    -0.70028677
    3
     0.33777078    2     2.57526386     3.69297065
                                       -4.76760461
     0.24253135    2    -4.63054123     8.87087502
                                      -10.49616087
     0.24331694    1    -9.40665268
BASIS_SETS
#########################################################################
#
# This is a library of molecularly optimised basis functions as described in the paper:
#
# Gaussian basis sets for accurate calculations on molecular systems
# in gas and condensed phases
#
# Joost VandeVondele and Juerg Hutter
# J. Chem. Phys. 127, 114105 (2007)
#
# URL: http://link.aip.org/link/?JCP/127/114105
# DOI: 10.1063/1.2770708
#
###########################################
 H  DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q1
 1
 2 0 1 7 2 1
     11.478000339908  0.024916243200 -0.012512421400  0.024510918200
      3.700758562763  0.079825490000 -0.056449071100  0.058140794100
      1.446884268432  0.128862675300  0.011242684700  0.444709498500
      0.716814589696  0.379448894600 -0.418587548300  0.646207973100
      0.247918564176  0.324552432600  0.590363216700  0.803385018200
      0.066918004004  0.037148121400  0.438703133000  0.892971208700
      0.021708243634 -0.001125195500 -0.059693171300  0.120101316500
 C  DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q4
 1
 2 0 2 7 2 2 1
      6.132624767898 -0.105576563700  0.024850587600  0.035098108400 -0.056712999000  0.037469425800
      2.625196064782 -0.174866621100  0.147440856000  0.114197930900 -0.076743951500  0.071047574800
      1.045456957247  0.064464981400 -0.421418379200  0.215908137300 -0.528056757000  0.619330561200
      0.478316330874  0.830447035300  0.823051336800  0.355929151000  0.394594045700  0.710730857000
      0.178617414302  0.371911373800  0.184880712100  0.271541842000  0.721247475800  0.389148235000
      0.075144725465  0.006174464000 -0.742086051600  0.056256557700  0.733902531700  0.346374124100
      0.030286753006  0.008966477300  0.083382192000  0.004998059700  0.248172175500 -0.005142430900
 O  DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q6
 1
 2 0 2 7 2 2 1
     12.015954705512 -0.060190841200  0.065738617900  0.036543638800 -0.034210557400  0.014807054400
      5.108150287385 -0.129597923300  0.110885902200  0.120927648700 -0.120619770900  0.068186159300
      2.048398039874  0.118175889400 -0.053732406400  0.251093670300 -0.213719464600  0.290576499200
      0.832381575582  0.462964485000 -0.572670666200  0.352639910300 -0.473674858400  1.063344189500
      0.352316246455  0.450353782600  0.186760006700  0.294708645200  0.484848376400  0.307656114200
      0.142977330880  0.092715833600  0.387201458600  0.173039869300  0.717465919700  0.318346834400
       0.046760918300 -0.000255945800  0.003825849600  0.009726110600  0.032498979400 -0.005771736600
 Ti DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q12
 1
 2 0 3 6 3 2 2 1
      7.884569925997  0.004750577412 -0.002690702837  0.075105591562 -0.108736525246  0.023185061556  0.052842407451 -0.038307431199 -0.002442658125
      3.894698463070  0.499503858222  0.103956524568  0.048602853477  0.100912855636 -0.027189036213  0.195986532018 -0.076880250937  0.013119020987
      1.513588828959 -0.664995883766 -0.256641947580  0.079732563787  0.527328996047 -0.230044390357  0.330343722079 -0.242486488988 -0.206817889885
      0.596768079836 -0.726044574739 -0.451591547817  1.660896378972  0.468197803110 -0.126795185046  0.396808432313 -0.118369379707 -0.546596492823
      0.222222125842 -0.029011079755  0.165167622946 -2.748651632733  0.077640626075  0.343517279356  0.347092399871  0.038099375809 -0.279145975103
      0.077078461321  0.075171747143  0.993127316430  1.368227638651 -0.007523238420  0.946960702315  0.132320900948  1.046553050597  0.934394052863
mode1.xyz
116

Ti       -0.0179479198       -0.0078042700       -0.0922850421
O         0.4497915479        0.0007412647        1.9321232563
Ti       -1.4316444492       -0.0089893346        2.8221490912
O        -1.7887110897        0.0007867236        0.7998892697
O        -3.2081345298        0.0411605531        3.6695321087
O        -1.8010755493       -1.8874663742        2.8216777686
Ti       -3.7269830403       -1.9006613639        3.6517557753
O         0.3830863054       -1.8910765741       -0.0700021876
Ti        3.7557586944       -1.8917451634        2.9143676586
O         3.3146470921       -0.0011081937        2.8729289358
O        -4.6680663094       -1.8855446073        2.0338712494
O        -5.4086768695       -1.8843459443        4.3991860126
Ti       -0.0282285127       -3.7757033787       -0.0787156736
O         0.4462623263       -3.7813137083        1.9359917441
Ti       -1.3999537875       -3.7707056149        2.8874421519
O        -1.7903153040       -3.7850263943        0.8021001791
O        -3.2390175951       -3.7978185279        3.6716494047
O        -1.7864035184       -5.6734792481        2.8627360747
Ti       -3.7357623244       -5.6788609282        3.4482649850
O         0.3837694100       -5.6723382681       -0.0690470865
Ti        3.7205660980       -5.6668034549        2.9114784222
O         3.3236114384       -3.7787921003        2.8721776992
O        -4.6689995455       -5.6807480198        1.9358553242
O        -5.3525041570       -5.6742752842        4.3359372112
Ti       -0.0314402214        3.7828933451       -0.0777664638
O         0.4518754735        3.7839662632        1.9399715530
Ti       -1.3792280628        3.7857276911        2.9025413153
O        -1.7909627210        3.7866794195        0.8027290293
O        -3.2026665631        3.7827561658        3.7306777258
O        -1.7857471998        1.9013100770        2.8154049594
Ti       -3.7307612355        1.9120465523        3.4387577457
O         0.3836352141        1.8909325251       -0.0691199251
Ti        3.7223424203        1.8887162901        2.9133081650
O         3.3250830331        3.7807500488        2.8687333178
O        -4.6728325926        1.9008997868        1.9326739591
O        -5.3457700344        1.8899459254        4.3344454640
Ti       -1.4852085406       -0.0011927086       -3.7100466053
O        -1.0850586016       -0.0008795951       -1.6147031707
Ti       -2.8526945884       -0.0039467894       -0.7412906371
O        -3.3269327110       -0.0004491456       -2.7420242486
O        -4.7289708978       -0.0017641392       -0.0618098107
O        -3.2591453480       -1.8898583454       -0.7264179834
Ti       -5.1372070666       -1.8918692243       -0.0012386637
O        -1.0878410276       -1.8908975100       -3.6681494905
Ti        2.2953566326       -1.8945802968       -0.7324918911
O         1.8572641703       -0.0016921856       -0.7344045642
O         4.0371444331       -1.8910414726       -1.5881377025
O         3.3210868792       -1.8907741455        0.8191885244
Ti       -1.4878179598       -3.7811586802       -3.7059227721
O        -1.0853532342       -3.7809408508       -1.6116052274
Ti       -2.8450252555       -3.7788195849       -0.7274776599
O        -3.3267379004       -3.7812381637       -2.7423527944
O        -4.7300872942       -3.7790968457       -0.0598090260
O        -3.2604741093       -5.6718710426       -0.7338292499
Ti       -5.1447866872       -5.6729502955       -0.0741564861
O        -1.0884608345       -5.6727912820       -3.6676316873
Ti        2.2684209803       -5.6717142765       -0.7217304029
O         1.8574125893       -3.7804564443       -0.7330818756
O         4.0285990372       -5.6721054737       -1.6077890803
O         3.3201243312       -5.6722897918        0.8087243331
Ti       -1.4884820434        3.7822906244       -3.7073217712
O        -1.0847762013        3.7818636329       -1.6113017246
Ti       -2.8439453199        3.7841411650       -0.7265400935
O        -3.3267270296        3.7819066970       -2.7433025606
O        -4.7312054524        3.7823723470       -0.0697069103
O        -3.2595288817        1.8897668415       -0.7334187674
Ti       -5.1446141745        1.8933189943       -0.0754881482
O        -1.0885182339        1.8906776867       -3.6679434552
Ti        2.2687722606        1.8941648243       -0.7213872473
O         1.8555780589        3.7824519637       -0.7335160805
O         4.0283551896        1.8906904137       -1.6083035670
O         3.3194888527        1.8901215845        0.8082989311
Ti        1.3702533850       -0.0107406935        3.4478828397
O        -2.6375196242       -0.0002691731       -5.1384544425
Ti       -4.2555253076       -0.0004346746       -4.2635860836
O        -0.2706997157       -0.0070914550        4.3327078320
O         4.0252034756       -0.0000815787       -3.6655962284
O        -4.7789243271       -1.8904283625       -4.5262265362
Ti        3.6276350884       -1.8913012322       -3.6941431294
O         1.8693336769       -1.8883429262        3.7243207414
Ti        0.8648978359       -1.8921733057       -4.2643698117
O         0.3356892769       -0.0005951329       -4.5283168344
O         2.4831990038       -1.8910320844       -5.1341360953
O         1.7891597814       -1.8911498456       -2.7417208102
Ti        1.3675607179       -3.7714249561        3.4584460387
O        -2.6361368408       -3.7817733748       -5.1377491017
Ti       -4.2537976019       -3.7816703567       -4.2621660812
O        -0.2527486810       -3.7773208994        4.3296691681
O         4.0251551834       -3.7817133665       -3.6656274881
O        -4.7792586102       -5.6728660382       -4.5273909859
Ti        3.6247553952       -5.6729206250       -3.7048960624
O         1.9006169442       -5.6721819263        3.7282320026
Ti        0.8602204280       -5.6728510136       -4.2616392365
O         0.3358111887       -3.7815283986       -4.5276229355
O         2.4785034911       -5.6729185089       -5.1373985723
O         1.7869078663       -5.6728807589       -2.7423620036
Ti        1.3817457800        3.7823928879        3.4589497419
O        -2.6363646230        3.7820140473       -5.1385122329
Ti       -4.2543090361        3.7822671573       -4.2626609244
O        -0.2374835922        3.7781640807        4.3379058406
O         4.0248222240        3.7818879520       -3.6667895479
O        -4.7794862202        1.8903770813       -4.5277962247
Ti        3.6243254290        1.8913422637       -3.7051707738
O         1.8974839341        1.8882474143        3.7289879155
Ti        0.8600377417        1.8920214690       -4.2620560393
O         0.3346421543        3.7821159876       -4.5275899679
O         2.4782941685        1.8909856222       -5.1376874872
O         1.7866749487        1.8910410218       -2.7427494459
H        -3.2770955004       -2.4268873548        8.1687296457
C        -3.1978647566       -1.3575831172        7.9359146369 
H        -4.2239524320       -0.9733256879        7.8414028480
H        -2.6752907472       -0.8249390527        8.7355765151
C        -2.5132448898       -1.1924834089        6.6141051521 
O        -2.8755597850       -1.8460118394        5.6163779603
O        -1.5275649623       -0.3212592281        6.6009413157
H        -1.0670534373       -0.2549619720        5.6840567874
mode2.xyz
116

Ti        0.0150786099       -0.0030604155       -0.2374201259
O         0.4515580466       -0.0646282100        1.8001155831
Ti       -1.5073356783       -0.0021026124        2.5525864818
O        -1.7759961007       -0.0002275800        0.6680111337
O        -3.3291162152       -0.0023490698        3.0696212715
O        -1.7197127142       -1.8809866556        2.8642842575
Ti       -3.6978004404       -1.8661667177        3.6084326925
O         0.3785074831       -1.8945596770       -0.1980298452
Ti        3.7996574045       -1.9219539316        2.8301270999
O         3.3305054330       -0.0058364403        2.7942261562
O        -4.6900333011       -1.9659285303        1.9448925419
O        -5.3925681292       -1.8976344334        4.3248895668
Ti       -0.0283064667       -3.7737024590       -0.1507446117
O         0.4475870469       -3.7803762159        1.8621586431
Ti       -1.3713031978       -3.7725215345        2.8511642577
O        -1.7912822225       -3.7729870345        0.7436262925
O        -3.1963784791       -3.7804631987        3.6648868231
O        -1.7705984874       -5.6752809020        2.8039139185
Ti       -3.7092032911       -5.6725438342        3.3897938268
O         0.3841910583       -5.6739517448       -0.1381224421
Ti        3.7513121067       -5.6747221635        2.8551954028
O         3.3367138059       -3.7840186471        2.8127851513
O        -4.6560725160       -5.6733549533        1.8776383238
O        -5.3204369054       -5.6669271369        4.2778026483
Ti       -0.0266777619        3.7696389407       -0.1491534163
O         0.4524897086        3.7857220830        1.8631418152
Ti       -1.3730627656        3.7742135603        2.8371003388
O        -1.7905256319        3.7786525562        0.7422177730
O        -3.1948630000        3.7795989881        3.6670918260
O        -1.7343662633        1.8899845272        2.8090040137
Ti       -3.6974632076        1.8668219133        3.5884163764
O         0.3822543310        1.8874843004       -0.1432095900
Ti        3.7864567490        1.9054527096        2.8508016360
O         3.3675002865        3.7799021368        2.8626057027
O        -4.6840457398        1.9746044749        1.9466850498
O        -5.3729095331        1.8414022655        4.3320391075
Ti       -1.5079668291       -0.0008456767       -3.7989215478
O        -1.0951317039        0.0022938033       -1.7345576883
Ti       -2.8929121223       -0.0000735048       -0.8782772455
O        -3.3736661811        0.0005357865       -2.8128806833
O        -4.7193863680        0.0001570116       -0.0748056115
O        -3.2632860440       -1.8860154449       -0.7956216654
Ti       -5.1307996411       -1.8978086035       -0.0398179095
O        -1.1320787396       -1.8909803808       -3.7440163178
Ti        2.3133857413       -1.9061341614       -0.8099170994
O         1.8786839357        0.0011314062       -0.8069543100
O         4.0385009963       -1.8895616393       -1.6570045786
O         3.3115055560       -1.8920970172        0.7501369741
Ti       -1.5256127358       -3.7819843403       -3.7701763163
O        -1.0940683369       -3.7869847697       -1.6789541127
Ti       -2.8425313294       -3.7819322313       -0.7839726892
O        -3.3422315516       -3.7760564219       -2.8030699366
O        -4.7315665522       -3.7831312336       -0.1321164185
O        -3.2580399316       -5.6728032840       -0.7985618810
Ti       -5.1462151180       -5.6726106968       -0.1400092932
O        -1.1340144859       -5.6732616791       -3.7388880843
Ti        2.2670101177       -5.6749205566       -0.7762329495
O         1.8631140907       -3.7853073574       -0.7974118985
O         4.0263575475       -5.6730177766       -1.6715945206
O         3.3250517248       -5.6784227751        0.7515944134
Ti       -1.5248867442        3.7818848512       -3.7712820230
O        -1.0907299886        3.7812336768       -1.6778258037
Ti       -2.8428177895        3.7841675976       -0.7861032158
O        -3.3397902383        3.7762483047       -2.8026235400
O        -4.7304156316        3.7842200412       -0.1318958639
O        -3.2645051173        1.8869138058       -0.7933488063
Ti       -5.1241443302        1.8993249071       -0.0252297449
O        -1.1314283131        1.8906347021       -3.7440419862
Ti        2.3185671036        1.9017475834       -0.7833845676
O         1.8597419566        3.7800089897       -0.7974665372
O         4.0344536794        1.8895028649       -1.6315658326
O         3.3098310076        1.8936248995        0.7823280807
Ti        1.4537853090       -0.0347286638        3.2604875735
O        -2.6845024000        0.0000746592       -5.2147510734
Ti       -4.2967571219        0.0018586454       -4.3442818967
O        -0.2511143909        0.1328085915        4.2720687411
O         3.9819696258        0.0012627538       -3.7355131655
O        -4.8038476957       -1.8889916108       -4.5923792314
Ti        3.5953547314       -1.8907810205       -3.7642624098
O         1.8553660493       -1.8815919187        3.6062633048
Ti        0.8351449362       -1.8959349617       -4.3196742869
O         0.3119042183       -0.0001283684       -4.5915870901
O         2.4377532123       -1.8915585194       -5.2027330310
O         1.7783437087       -1.8888222418       -2.8082665928
Ti        1.3904951140       -3.7857957693        3.3690175525
O        -2.6814201117       -3.7831847959       -5.2025558657
Ti       -4.2854691947       -3.7801054852       -4.3136778334
O        -0.2074321278       -3.7970194791        4.2709539045
O         3.9820256895       -3.7800854351       -3.7356644708
O        -4.7961377238       -5.6736624399       -4.5471769110
Ti        3.5917963887       -5.6730897244       -3.7666434973
O         1.9069112439       -5.6781980199        3.6136248160
Ti        0.8312484616       -5.6732029738       -4.3044789530
O         0.3186267326       -3.7822693739       -4.5479829736
O         2.4335197920       -5.6733247069       -5.1986406627
O         1.7786689446       -5.6734212363       -2.7982114552
Ti        1.3984968329        3.7644681343        3.3685503422
O        -2.6815455972        3.7828337111       -5.2024703087
Ti       -4.2855071694        3.7788568387       -4.3128750844
O        -0.2044150611        3.7319133608        4.2704391005
O         3.9827213914        3.7789077586       -3.7330838039
O        -4.8039829955        1.8898269577       -4.5907748518
Ti        3.5899147654        1.8912350407       -3.7590482617
O         1.8739898095        1.8720733323        3.5992207033
Ti        0.8344557677        1.8954291350       -4.3129140724
O         0.3192643376        3.7819866970       -4.5466934222
O         2.4382493211        1.8919495801       -5.1986096411
O         1.7788752457        1.8885973165       -2.8025129463
H        -1.3211320733       -0.5901398003        7.3622691450
C        -2.2774669737       -0.0487846563        7.3616031246
H        -2.9713818519       -0.6195053843        7.9928436643
H        -2.1415146457        0.9598101494        7.7628564958
C        -2.8081585120       -0.0061954447        5.9550273922
O        -3.0662415287       -1.1345711119        5.4074245732
O        -2.9500441444        1.1398319329        5.4010622063
H        -0.3897742635        1.0153182782        4.6757696096
relaxed_slab.xyz
108

Ti       -0.0196732895        0.0000918380       -0.1416465741
O         0.4723754303       -0.0000571398        1.8571329054
Ti       -1.3559074694        0.0003150892        2.8298591619
O        -1.7917634261        0.0000042454        0.7442319008
O        -3.2061730694        0.0000443286        3.6117036980
O        -1.7223354624       -1.8909532145        2.7851161998
Ti       -3.7072315168       -1.8909277477        3.3703342068
O         0.3901175533       -1.8910690189       -0.0994036486
Ti        3.7576915752       -1.8911397898        2.8299030461
O         3.3911899157       -0.0000297653        2.7851197963
O        -4.6411313870       -1.8910064850        1.8571563829
O        -5.3047652050       -1.8910036123        4.2598669896
Ti       -0.0207144299       -3.7823141879       -0.1416512835
O         0.4723696865       -3.7819602214        1.8571632167
Ti       -1.3558005079       -3.7816819453        2.8299339589
O        -1.7918422000       -3.7820015816        0.7441593253
O        -3.2061826485       -3.7819698735        3.6117085462
O        -1.7223161680       -5.6729527662        2.7851217809
Ti       -3.7072713992       -5.6728628337        3.3703727335
O         0.3900935320       -5.6730270615       -0.0995105980
Ti        3.7576114879       -5.6731618014        2.8298917840
O         3.3911555573       -3.7820325584        2.7851125323
O        -4.6411391763       -5.6729793650        1.8571500583
O        -5.3047626840       -5.6729983041        4.2598661875
Ti       -0.0207062513        3.7820375711       -0.1416644578
O         0.4723667071        3.7820212636        1.8571594186
Ti       -1.3558175168        3.7823572855        2.8299239946
O        -1.7918406363        3.7820160635        0.7441611103
O        -3.2061760961        3.7820487555        3.6117151381
O        -1.7223390903        1.8910430419        2.7851256747
Ti       -3.7072222362        1.8911540810        3.3703550256
O         0.3900787901        1.8910478727       -0.0995442876
Ti        3.7576703685        1.8908168863        2.8299163973
O         3.3911596509        3.7819754093        2.7851182559
O        -4.6411291967        1.8910010642        1.8571457837
O        -5.3047626859        1.8909942468        4.2598643270
Ti       -1.5161932358       -0.0000035504       -3.7515860671
O        -1.0530794682        0.0000373091       -1.6689815731
Ti       -2.8375929946        0.0000125387       -0.7827105109
O        -3.3233955054        0.0000075742       -2.7856149033
O        -4.7234020378        0.0000127699       -0.0994911115
O        -3.2337827875       -1.8909157918       -0.8262536553
Ti       -5.1341235465       -1.8905124453       -0.1416968775
O        -1.1292018546       -1.8909984997       -3.7065474973
Ti        2.2748016978       -1.8914513528       -0.7826856888
O         1.8795957531        0.0000110574       -0.8262556229
O         4.0603419699       -1.8909917501       -1.6690496877
O         3.3216577066       -1.8910129398        0.7441708384
Ti       -1.5162127974       -3.7820082245       -3.7515130590
O        -1.0531792321       -3.7820330939       -1.6690695233
Ti       -2.8387264069       -3.7816366671       -0.7827254195
O        -3.3234176494       -3.7820188222       -2.7855855806
O        -4.7234014156       -3.7819208779       -0.0994918740
O        -3.2338808261       -5.6729547241       -0.8262577269
Ti       -5.1337085619       -5.6728210746       -0.1416253758
O        -1.1292133652       -5.6729973337       -3.7065579586
Ti        2.2753347025       -5.6730893793       -0.7827232123
O         1.8797137276       -3.7820716331       -0.8262204725
O         4.0603607770       -5.6729995420       -1.6690205190
O         3.3216956874       -5.6729959521        0.7441905856
Ti       -1.5161826614        3.7820038515       -3.7514972186
O        -1.0531788180        3.7820037637       -1.6690627781
Ti       -2.8387418861        3.7820263057       -0.7827288483
O        -3.3234140545        3.7820124036       -2.7855756894
O        -4.7234083483        3.7819922024       -0.0995146234
O        -3.2338028141        1.8909665882       -0.8262616531
Ti       -5.1337579488        1.8907071790       -0.1416523764
O        -1.1292026624        1.8909963190       -3.7065514064
Ti        2.2752985947        1.8913614389       -0.7827305566
O         1.8797190226        3.7820105992       -0.8262619610
O         4.0603653380        1.8909999509       -1.6690263461
O         3.3217002712        1.8910054858        0.7441955377
Ti        1.4062179326       -0.0001039492        3.3703877757
O        -2.6647908793       -0.0000005289       -5.1851681482
Ti       -4.2783192715       -0.0000103698       -4.2957638096
O        -0.1912654580       -0.0000031849        4.2598577618
O         3.9842928859       -0.0000042475       -3.7065509870
O        -4.8135555127       -1.8910056257       -4.5423161488
Ti        3.5973231742       -1.8910334733       -3.7514938579
O         1.9073102520       -1.8910183747        3.6116941841
Ti        0.8351562937       -1.8910134280       -4.2957834807
O         0.2999501886        0.0000014389       -4.5423282903
O         2.4486923948       -1.8909965776       -5.1851300375
O         1.7901009453       -1.8909751422       -2.7855702026
Ti        1.4062978231       -3.7820651787        3.3703408897
O        -2.6648159269       -3.7820081917       -5.1851412951
Ti       -4.2783858420       -3.7820055719       -4.2957974907
O        -0.1912655926       -3.7819815684        4.2598700174
O         3.9842992272       -3.7820123323       -3.7065446628
O        -4.8135568089       -5.6730065260       -4.5423203244
Ti        3.5973007930       -5.6730640942       -3.7515344719
O         1.9073227407       -5.6730308667        3.6117054398
Ti        0.8351415277       -5.6729732703       -4.2957889394
O         0.2999374565       -3.7820001861       -4.5423268691
O         2.4486955431       -5.6730031698       -5.1851504663
O         1.7900885384       -5.6729995069       -2.7856065156
Ti        1.4062636238        3.7818822883        3.3703472345
O        -2.6648052713        3.7820054054       -5.1851376998
Ti       -4.2783535642        3.7819717438       -4.2957964866
O        -0.1912672794        3.7820176010        4.2598712038
O         3.9842996857        3.7819972148       -3.7065500902
O        -4.8135603835        1.8909955587       -4.5423217385
Ti        3.5972989622        1.8909274430       -3.7515400005
O         1.9073252382        1.8909600359        3.6117124490
Ti        0.8351502243        1.8910341251       -4.2957798103
O         0.2999353645        3.7820068984       -4.5423256737
O         2.4486964067        1.8909882434       -5.1851527864
O         1.7900926030        1.8909706946       -2.7855892400

–>

exercises/2017_ethz_mmm/c2h2_pdga.txt · Last modified: 2020/08/21 10:15 (external edit)