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exercises:2016_ethz_mmm:dye_tio

Dye anchoring to TiO$_2$

In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in Dye-Sensitized Solar Cells as an anchoring moiety to bind light harvesting dyes to semi-conducting substrates. We will therefore use acetic acid as a model of the more complex dye molecules, as done in this paper: 10.1021/jp4117563

1. Task: Familiarize yourself

The coordinates of the two binding modes are provided to you as mode1.xyz and mode2.xyz. Visualize the two geometries with VMD and familiarize yourself with the system.

2. Task: Bond induced density differences

Compute the density difference induced by the bonding for the first binding mode. For this you will have to run three separate energy calculations:

  1. combined system bound in the first mode (file mode1.xyz)
  2. lone acetic acid molecule (just remove slab's coordinates from mode1.xyz)
  3. lone TiO$_2$ slab (just remove the acid's coordinates from mode1.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 large TiO$_2$ slab should be run on 16 nodes with bsub -n 16.

To process the cube files we are going to use the cubecruncher tool. It is part of CP2K, but not installed on euler. Therefore, you'll have to download and compile it yourself:

you@eulerX ~$ svn checkout http://svn.code.sf.net/p/cp2k/code/trunk/cp2k/tools/cubecruncher
you@eulerX ~$ cd cubecruncher
you@eulerX ~$ make
you@eulerX ~$ ./cubecruncher.x -help

Now subtract the densities of the lone systems from the bonded system:

you@eulerX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract mode1_acid-ELECTRON_DENSITY-1_0.cube -o tmp.cube
you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract mode1_slab-ELECTRON_DENSITY-1_0.cube -o mode1_delta.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 mode1_delta.cube -o mode1_delta-centered.cube

You can visualize the resulting file mode1_delta-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 for both binding modes:

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

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

  1. lone acetic acid molecule (run geometry optimization, use energy of last step)
  2. lone TiO$_2$ slab (you can use the already geometry optimized coordinates from relaxed_slab.xyz at the end of the exercise)
  3. combined system bound in the first mode (can be reused from previous task)
  4. combined system bound in the second mode (file mode2.xyz)

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. This has been covered in a previous exercise.

Questions

  • Sketch briefly the two binding modes.
  • Report the system energy for the two binding modes, lone slab, and lone acid molecule.
  • Which binding mode is more stable?
  • 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 XYZ-files can not be included into CP2K's input directly. You have to convert them to .coord files by removing the first line, which states the number of atoms, and the following empty comment line.

mode1.inp
&GLOBAL
  ! change name for each different run performed
  PROJECT mode1
  RUN_TYPE ENERGY             
&END GLOBAL

&FORCE_EVAL
  METHOD Quickstep
  &DFT

    &PRINT
       &E_DENSITY_CUBE        !  section to print the electronic density of the system (Task 2)
       &END E_DENSITY_CUBE
    &END

    BASIS_SET_FILE_NAME BASIS_SETS            
    ! This keyword refers the input to an external basis file, which has to be in the same directory as this input file
    POTENTIAL_FILE_NAME POTENTIALS            
    ! This keyword refers the input to an external potential file, which has to be in the same directory as this input file

    &SCF                                      ! Ensures convergence of SCF and simulations stability. This section should not be changed
      MAX_SCF 50
      &OT
        PRECONDITIONER FULL_SINGLE_INVERSE
      &END OT
      &OUTER_SCF
        MAX_SCF 10
      &END
    &END SCF

    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC


  &END DFT
    
  &SUBSYS
    &CELL
      ABC 10.2270 11.3460 20.000
    &END CELL
    &COORD
    
! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this:
@INCLUDE 'mode1.coord'        ! The mode1.coord file must be present in the same directory as the input. 
                              ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning
 
   &END COORD
    &KIND H                                 ! All basis sets and potentials are looked up in the external files specified above.
      BASIS_SET DZVP-MOLOPT-GTH             ! search in the external basis file (specified above) the one named DZVP-MOLOPT-GTH for H.
      POTENTIAL GTH-PBE-q1                  ! search in the external potential file (specified above) the one named GTH-PBE-q1 for H.
    &END KIND
    &KIND C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
    &KIND Ti
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q12
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
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/2016_ethz_mmm/dye_tio.txt · Last modified: 2016/02/03 10:54 (external edit)