exercises:2017_ethz_mmm:dye_tio
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+ | ====== 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 [[wp> | ||
+ | {{ dye2.png? | ||
+ | |||
+ | ===== 1. Task: Familiarize yourself | ||
+ | The coordinates of the two binding modes are provided to you as '' | ||
+ | |||
+ | ===== 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 '' | ||
+ | - lone acetic acid molecule (just remove slab's coordinates from '' | ||
+ | - lone TiO$_2$ slab (just remove the acid's coordinates from '' | ||
+ | |||
+ | In order to output the electronic densities as cube files, your input file has to contain the following snipped: | ||
+ | < | ||
+ | &DFT | ||
+ | |||
+ | & | ||
+ | &END E_DENSITY_CUBE | ||
+ | &END | ||
+ | &END DFT | ||
+ | </ | ||
+ | |||
+ | <note tip> | ||
+ | The calculations involving the large TiO$_2$ slab should be run on 16 nodes with '' | ||
+ | </ | ||
+ | |||
+ | To process the cube files we are going to use the [[tools: | ||
+ | Therefore, you'll have to download and compile it yourself: | ||
+ | < | ||
+ | you@eulerX ~$ svn checkout http:// | ||
+ | you@eulerX ~$ cd cubecruncher | ||
+ | you@eulerX ~$ make | ||
+ | you@eulerX ~$ ./ | ||
+ | </ | ||
+ | |||
+ | Now subtract the densities of the lone systems from the bonded system: | ||
+ | < | ||
+ | you@eulerX ~$ ./ | ||
+ | you@eulerX ~$ ./ | ||
+ | </ | ||
+ | |||
+ | |||
+ | The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: | ||
+ | < | ||
+ | you@eulerX ~$ ./ | ||
+ | </ | ||
+ | |||
+ | You can visualize the resulting file '' | ||
+ | |||
+ | What you get should look similar to this: | ||
+ | {{ dye_tio_bonding_density.png? | ||
+ | |||
+ | ===== 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, | ||
+ | - lone TiO$_2$ slab (you can use the already geometry optimized coordinates from '' | ||
+ | - combined system bound in the first mode (can be reused from previous task) | ||
+ | - combined system bound in the second mode (file '' | ||
+ | |||
+ | <note important> | ||
+ | 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 | ||
+ | [[geometry_optimization|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 ===== | ||
+ | <note tip> 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, | ||
+ | |||
+ | <note warning> | ||
+ | The provided [[wp> | ||
+ | </ | ||
+ | |||
+ | |||
+ | <code - mode1.inp> | ||
+ | &GLOBAL | ||
+ | ! change name for each different run performed | ||
+ | PROJECT mode1 | ||
+ | RUN_TYPE ENERGY | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | METHOD Quickstep | ||
+ | &DFT | ||
+ | |||
+ | |||
+ | & | ||
+ | & | ||
+ | &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 | ||
+ | |||
+ | & | ||
+ | MAX_SCF 50 | ||
+ | &OT | ||
+ | PRECONDITIONER FULL_SINGLE_INVERSE | ||
+ | &END OT | ||
+ | & | ||
+ | MAX_SCF 10 | ||
+ | &END | ||
+ | &END SCF | ||
+ | |||
+ | &XC | ||
+ | & | ||
+ | &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 ' | ||
+ | ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning | ||
+ | |||
+ | & | ||
+ | &KIND H ! All basis sets and potentials are looked up in the external files specified above. | ||
+ | BASIS_SET DZVP-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE-q1 | ||
+ | &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 | ||
+ | |||
+ | </ | ||
+ | |||
+ | <code - 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, | ||
+ | # | ||
+ | # | ||
+ | # Potential for the PBE functional | ||
+ | # | ||
+ | ################################################################################ | ||
+ | # | ||
+ | H GTH-PBE-q1 | ||
+ | 1 | ||
+ | | ||
+ | 0 | ||
+ | # | ||
+ | C GTH-PBE-q4 | ||
+ | 2 2 | ||
+ | | ||
+ | 2 | ||
+ | | ||
+ | | ||
+ | # | ||
+ | O GTH-PBE-q6 | ||
+ | 2 4 | ||
+ | | ||
+ | 2 | ||
+ | | ||
+ | | ||
+ | # | ||
+ | Ti GTH-PBE-q12 | ||
+ | 4 6 2 | ||
+ | | ||
+ | 3 | ||
+ | | ||
+ | | ||
+ | | ||
+ | -10.49616087 | ||
+ | | ||
+ | |||
+ | </ | ||
+ | |||
+ | <code - 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:// | ||
+ | # DOI: 10.1063/ | ||
+ | # | ||
+ | ########################################### | ||
+ | | ||
+ | 1 | ||
+ | 2 0 1 7 2 1 | ||
+ | | ||
+ | 3.700758562763 | ||
+ | 1.446884268432 | ||
+ | 0.716814589696 | ||
+ | 0.247918564176 | ||
+ | 0.066918004004 | ||
+ | 0.021708243634 -0.001125195500 -0.059693171300 | ||
+ | | ||
+ | 1 | ||
+ | 2 0 2 7 2 2 1 | ||
+ | 6.132624767898 -0.105576563700 | ||
+ | 2.625196064782 -0.174866621100 | ||
+ | 1.045456957247 | ||
+ | 0.478316330874 | ||
+ | 0.178617414302 | ||
+ | 0.075144725465 | ||
+ | 0.030286753006 | ||
+ | | ||
+ | 1 | ||
+ | 2 0 2 7 2 2 1 | ||
+ | | ||
+ | 5.108150287385 -0.129597923300 | ||
+ | 2.048398039874 | ||
+ | 0.832381575582 | ||
+ | 0.352316246455 | ||
+ | 0.142977330880 | ||
+ | | ||
+ | Ti DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q12 | ||
+ | 1 | ||
+ | 2 0 3 6 3 2 2 1 | ||
+ | 7.884569925997 | ||
+ | 3.894698463070 | ||
+ | 1.513588828959 -0.664995883766 -0.256641947580 | ||
+ | 0.596768079836 -0.726044574739 -0.451591547817 | ||
+ | 0.222222125842 -0.029011079755 | ||
+ | 0.077078461321 | ||
+ | |||
+ | </ | ||
+ | |||
+ | <code - mode1.xyz> | ||
+ | 116 | ||
+ | |||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7887110897 | ||
+ | O -3.2081345298 | ||
+ | O -1.8010755493 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7557586944 | ||
+ | O | ||
+ | O -4.6680663094 | ||
+ | O -5.4086768695 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7903153040 | ||
+ | O -3.2390175951 | ||
+ | O -1.7864035184 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7205660980 | ||
+ | O | ||
+ | O -4.6689995455 | ||
+ | O -5.3525041570 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7909627210 | ||
+ | O -3.2026665631 | ||
+ | O -1.7857471998 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7223424203 | ||
+ | O | ||
+ | O -4.6728325926 | ||
+ | O -5.3457700344 | ||
+ | Ti | ||
+ | O -1.0850586016 | ||
+ | Ti | ||
+ | O -3.3269327110 | ||
+ | O -4.7289708978 | ||
+ | O -3.2591453480 | ||
+ | Ti | ||
+ | O -1.0878410276 | ||
+ | Ti 2.2953566326 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0853532342 | ||
+ | Ti | ||
+ | O -3.3267379004 | ||
+ | O -4.7300872942 | ||
+ | O -3.2604741093 | ||
+ | Ti | ||
+ | O -1.0884608345 | ||
+ | Ti 2.2684209803 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0847762013 | ||
+ | Ti | ||
+ | O -3.3267270296 | ||
+ | O -4.7312054524 | ||
+ | O -3.2595288817 | ||
+ | Ti | ||
+ | O -1.0885182339 | ||
+ | Ti 2.2687722606 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.3702533850 | ||
+ | O -2.6375196242 | ||
+ | Ti | ||
+ | O -0.2706997157 | ||
+ | O | ||
+ | O -4.7789243271 | ||
+ | Ti 3.6276350884 | ||
+ | O | ||
+ | Ti 0.8648978359 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.3675607179 | ||
+ | O -2.6361368408 | ||
+ | Ti | ||
+ | O -0.2527486810 | ||
+ | O | ||
+ | O -4.7792586102 | ||
+ | Ti 3.6247553952 | ||
+ | O | ||
+ | Ti 0.8602204280 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.3817457800 | ||
+ | O -2.6363646230 | ||
+ | Ti | ||
+ | O -0.2374835922 | ||
+ | O | ||
+ | O -4.7794862202 | ||
+ | Ti 3.6243254290 | ||
+ | O | ||
+ | Ti 0.8600377417 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | H -3.2770955004 | ||
+ | C -3.1978647566 | ||
+ | H -4.2239524320 | ||
+ | H -2.6752907472 | ||
+ | C -2.5132448898 | ||
+ | O -2.8755597850 | ||
+ | O -1.5275649623 | ||
+ | H -1.0670534373 | ||
+ | |||
+ | </ | ||
+ | |||
+ | <code - mode2.xyz> | ||
+ | 116 | ||
+ | |||
+ | Ti 0.0150786099 | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7759961007 | ||
+ | O -3.3291162152 | ||
+ | O -1.7197127142 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7996574045 | ||
+ | O | ||
+ | O -4.6900333011 | ||
+ | O -5.3925681292 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7912822225 | ||
+ | O -3.1963784791 | ||
+ | O -1.7705984874 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7513121067 | ||
+ | O | ||
+ | O -4.6560725160 | ||
+ | O -5.3204369054 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7905256319 | ||
+ | O -3.1948630000 | ||
+ | O -1.7343662633 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7864567490 | ||
+ | O | ||
+ | O -4.6840457398 | ||
+ | O -5.3729095331 | ||
+ | Ti | ||
+ | O -1.0951317039 | ||
+ | Ti | ||
+ | O -3.3736661811 | ||
+ | O -4.7193863680 | ||
+ | O -3.2632860440 | ||
+ | Ti | ||
+ | O -1.1320787396 | ||
+ | Ti 2.3133857413 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0940683369 | ||
+ | Ti | ||
+ | O -3.3422315516 | ||
+ | O -4.7315665522 | ||
+ | O -3.2580399316 | ||
+ | Ti | ||
+ | O -1.1340144859 | ||
+ | Ti 2.2670101177 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0907299886 | ||
+ | Ti | ||
+ | O -3.3397902383 | ||
+ | O -4.7304156316 | ||
+ | O -3.2645051173 | ||
+ | Ti | ||
+ | O -1.1314283131 | ||
+ | Ti 2.3185671036 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.4537853090 | ||
+ | O -2.6845024000 | ||
+ | Ti | ||
+ | O -0.2511143909 | ||
+ | O | ||
+ | O -4.8038476957 | ||
+ | Ti 3.5953547314 | ||
+ | O | ||
+ | Ti 0.8351449362 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.3904951140 | ||
+ | O -2.6814201117 | ||
+ | Ti | ||
+ | O -0.2074321278 | ||
+ | O | ||
+ | O -4.7961377238 | ||
+ | Ti 3.5917963887 | ||
+ | O | ||
+ | Ti 0.8312484616 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.3984968329 | ||
+ | O -2.6815455972 | ||
+ | Ti | ||
+ | O -0.2044150611 | ||
+ | O | ||
+ | O -4.8039829955 | ||
+ | Ti 3.5899147654 | ||
+ | O | ||
+ | Ti 0.8344557677 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | H -1.3211320733 | ||
+ | C -2.2774669737 | ||
+ | H -2.9713818519 | ||
+ | H -2.1415146457 | ||
+ | C -2.8081585120 | ||
+ | O -3.0662415287 | ||
+ | O -2.9500441444 | ||
+ | H -0.3897742635 | ||
+ | </ | ||
+ | |||
+ | <code - relaxed_slab.xyz> | ||
+ | 108 | ||
+ | |||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7917634261 | ||
+ | O -3.2061730694 | ||
+ | O -1.7223354624 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7576915752 | ||
+ | O | ||
+ | O -4.6411313870 | ||
+ | O -5.3047652050 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7918422000 | ||
+ | O -3.2061826485 | ||
+ | O -1.7223161680 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7576114879 | ||
+ | O | ||
+ | O -4.6411391763 | ||
+ | O -5.3047626840 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7918406363 | ||
+ | O -3.2061760961 | ||
+ | O -1.7223390903 | ||
+ | Ti | ||
+ | O | ||
+ | Ti 3.7576703685 | ||
+ | O | ||
+ | O -4.6411291967 | ||
+ | O -5.3047626859 | ||
+ | Ti | ||
+ | O -1.0530794682 | ||
+ | Ti | ||
+ | O -3.3233955054 | ||
+ | O -4.7234020378 | ||
+ | O -3.2337827875 | ||
+ | Ti | ||
+ | O -1.1292018546 | ||
+ | Ti 2.2748016978 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0531792321 | ||
+ | Ti | ||
+ | O -3.3234176494 | ||
+ | O -4.7234014156 | ||
+ | O -3.2338808261 | ||
+ | Ti | ||
+ | O -1.1292133652 | ||
+ | Ti 2.2753347025 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0531788180 | ||
+ | Ti | ||
+ | O -3.3234140545 | ||
+ | O -4.7234083483 | ||
+ | O -3.2338028141 | ||
+ | Ti | ||
+ | O -1.1292026624 | ||
+ | Ti 2.2752985947 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.4062179326 | ||
+ | O -2.6647908793 | ||
+ | Ti | ||
+ | O -0.1912654580 | ||
+ | O | ||
+ | O -4.8135555127 | ||
+ | Ti 3.5973231742 | ||
+ | O | ||
+ | Ti 0.8351562937 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.4062978231 | ||
+ | O -2.6648159269 | ||
+ | Ti | ||
+ | O -0.1912655926 | ||
+ | O | ||
+ | O -4.8135568089 | ||
+ | Ti 3.5973007930 | ||
+ | O | ||
+ | Ti 0.8351415277 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti 1.4062636238 | ||
+ | O -2.6648052713 | ||
+ | Ti | ||
+ | O -0.1912672794 | ||
+ | O | ||
+ | O -4.8135603835 | ||
+ | Ti 3.5972989622 | ||
+ | O | ||
+ | Ti 0.8351502243 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | </ |
exercises/2017_ethz_mmm/dye_tio.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1