exercises:2014_ethz_mmm:dye_tio
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exercise:dye_tio [2014/04/04 08:52] – oschuett | exercises:2014_ethz_mmm:dye_tio [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Dye anchoring to TiO$_2$ ====== | ====== 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> | + | 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> |
- | {{ :exercise:dye2.png? | + | {{ dye2.png? |
===== 1. Task: Familiarize yourself | ===== 1. Task: Familiarize yourself | ||
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To process the cube files we are going to use the cubecruncher tool. It is part of CP2K, but not installed on brutus. | 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 ''/ | + | Therefore, a compiled binary of the tool is provided at ''/ |
< | < | ||
you@brutusX ~$ ln -s / | you@brutusX ~$ ln -s / | ||
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Now subtract the densities of the lone systems from the bonded system: | Now subtract the densities of the lone systems from the bonded system: | ||
< | < | ||
- | you@brutusX ~$ cubecruncher.x -i mode1_combined.cube -subtract | + | you@brutusX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract |
- | you@brutusX ~$ cubecruncher.x -i tmp.cube -subtract | + | you@brutusX ~$ ./cubecruncher.x -i tmp.cube -subtract |
</ | </ | ||
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You can visualize the resulting file '' | You can visualize the resulting file '' | ||
+ | |||
+ | What you get should look similar to this: | ||
+ | {{ dye_tio_bonding_density.png? | ||
===== 3. Task: Bonding energies | ===== 3. Task: Bonding energies | ||
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For this you will need the energy values of four systems: | For this you will need the energy values of four systems: | ||
- | - lone acetic acid molecule (run geometry optimization | + | - 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 '' | - 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 first mode (can be reused from previous task) | ||
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<note important> | <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 | 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 | ||
- | [[exercise:geometry_optimization|previous exercise]]. | + | [[geometry_optimization|previous exercise]]. |
</ | </ | ||
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<note warning> | <note warning> | ||
- | The provided XYZ-files can not be included into CP2K's input directly. You first have to remove | + | The provided |
- | < | + | </note> |
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| | ||
! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this: | ! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this: | ||
- | @INCLUDE 'mode1_coord' | + | @INCLUDE 'mode1.coord' |
! The file should be similar to an *.xyz file but without the total number of atoms at the beginning | ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning | ||
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<code - mode1.xyz> | <code - mode1.xyz> | ||
- | Ti 0.0150786099 | + | 116 |
- | 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 -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> | ||
Ti | Ti | ||
O | O | ||
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O | 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 | H -1.3211320733 | ||
C -2.2774669737 | C -2.2774669737 | ||
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O -2.9500441444 | O -2.9500441444 | ||
H -0.3897742635 | H -0.3897742635 | ||
- | |||
</ | </ | ||
<code - relaxed_slab.xyz> | <code - relaxed_slab.xyz> | ||
- | Ti | + | 108 |
- | O | + | |
- | Ti | + | |
- | O -1.7878355710 | + | |
- | O -3.1920046188 | + | |
- | O -1.7392688578 | + | |
- | Ti | + | |
- | O | + | |
- | Ti 3.7648454616 | + | |
- | O | + | |
- | O -4.6517384122 | + | |
- | O -5.3048604582 | + | |
- | Ti | + | |
- | O | + | |
- | Ti | + | |
- | O -1.7878502749 | + | |
- | O -3.1920078900 | + | |
- | O -1.7391317134 | + | |
- | Ti | + | |
- | O | + | |
- | Ti 3.7645108291 | + | |
- | O | + | |
- | O -4.6518683783 | + | |
- | O -5.3048543483 | + | |
- | Ti | + | |
- | O | + | |
- | Ti | + | |
- | O -1.7878722642 | + | |
- | O -3.1920029890 | + | |
- | O -1.7392431026 | + | |
- | Ti | + | |
- | O | + | |
- | Ti 3.7647483625 | + | |
- | O | + | |
- | O -4.6518133313 | + | |
- | O -5.3048288292 | + | |
- | Ti | + | |
- | O -1.0884291790 | + | |
- | Ti | + | |
- | O -3.3377699606 | + | |
- | O -4.7315575216 | + | |
- | O -3.2582658881 | + | |
- | Ti | + | |
- | O -1.1370163008 | + | |
- | Ti 2.2684272586 | + | |
- | O | + | |
- | O | + | |
- | O | + | |
- | Ti | + | |
- | O -1.0884224454 | + | |
- | Ti | + | |
- | O -3.3378256175 | + | |
- | O -4.7314704529 | + | |
- | O -3.2583566629 | + | |
- | Ti | + | |
- | O -1.1370531089 | + | |
- | Ti 2.2691513647 | + | |
- | O | + | |
- | O | + | |
- | O | + | |
- | Ti | + | |
- | O -1.0883945790 | + | |
- | Ti | + | |
- | O -3.3378273935 | + | |
- | O -4.7314320343 | + | |
- | O -3.2583140921 | + | |
- | Ti | + | |
- | O -1.1370619143 | + | |
- | Ti 2.2691991364 | + | |
- | O | + | |
- | O | + | |
- | O | + | |
- | Ti 1.4115723468 | + | |
- | O -2.6848950906 | + | |
- | Ti | + | |
- | O -0.1913341931 | + | |
- | O | + | |
- | O -4.7977239298 | + | |
- | Ti 3.5861119961 | + | |
- | O | + | |
- | Ti 0.8253184367 | + | |
- | O | + | |
- | O | + | |
- | O | + | |
- | Ti 1.4122145794 | + | |
- | O -2.6849548157 | + | |
- | Ti | + | |
- | O -0.1913221230 | + | |
- | O | + | |
- | O -4.7977200607 | + | |
- | Ti 3.5861498714 | + | |
- | O | + | |
- | Ti 0.8253871242 | + | |
- | O | + | |
- | O | + | |
- | O | + | |
- | Ti 1.4120341934 | + | |
- | O -2.6849563408 | + | |
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- | O -0.1913429323 | + | |
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- | O -4.7976917037 | + | |
- | Ti 3.5862152261 | + | |
- | O | + | |
- | Ti 0.8254109865 | + | |
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- | O | + | |
- | O | + | |
+ | 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 | ||
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+ | O -4.6411391763 | ||
+ | O -5.3047626840 | ||
+ | Ti | ||
+ | O | ||
+ | Ti | ||
+ | O -1.7918406363 | ||
+ | O -3.2061760961 | ||
+ | O -1.7223390903 | ||
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+ | O | ||
+ | Ti 3.7576703685 | ||
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+ | O -4.6411291967 | ||
+ | O -5.3047626859 | ||
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+ | O -1.0530794682 | ||
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+ | O -3.3233955054 | ||
+ | O -4.7234020378 | ||
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+ | O -1.1292018546 | ||
+ | Ti 2.2748016978 | ||
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+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0531792321 | ||
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+ | O -3.3234176494 | ||
+ | O -4.7234014156 | ||
+ | O -3.2338808261 | ||
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+ | O -1.1292133652 | ||
+ | Ti 2.2753347025 | ||
+ | O | ||
+ | O | ||
+ | O | ||
+ | Ti | ||
+ | O -1.0531788180 | ||
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+ | O -3.3234140545 | ||
+ | O -4.7234083483 | ||
+ | O -3.2338028141 | ||
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+ | 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/2014_ethz_mmm/dye_tio.1396601530.txt.gz · Last modified: 2020/08/21 10:14 (external edit)