exercises:2014_ethz_mmm:dye_tio
Table of Contents
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 coordinate of the two binding modes are provided 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:
- combined system bound in the first mode (file
mode1.xyz) - lone acetic acid molecule (just remove slab's coordinates from
mode1.xyz) - 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 brutus.
Therefore, a compiled binary of the tool is provided at /cluster/home03/matl/schuetto/cubecruncher.x. Before invoking the cubecruncher, you have to load the cp2k module. To simplify the following steps you should create a symbolic link to it in your working directory:
you@brutusX ~$ ln -s /cluster/home03/matl/schuetto/cubecruncher.x .
Now subtract the densities of the lone systems from the bonded system:
you@brutusX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract mode1_acid-ELECTRON_DENSITY-1_0.cube -o tmp.cube you@brutusX ~$ ./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@brutusX ~$ 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:
- lone acetic acid molecule (run geometry optimization, use energy of last step)
- lone TiO$_2$ slab (you can use the already geometry optimized coordinates from
relaxed_slab.xyzat the end of the exercise) - combined system bound in the first mode (can be reused from previous task)
- 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 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- mode2.xyz
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exercises/2014_ethz_mmm/dye_tio.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1