exercises:2014_ethz_mmm:dye_tio
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exercise:dye_tio [2014/04/04 08:43] – 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 / | ||
Line 37: | Line 37: | ||
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]]. |
</ | </ | ||
Line 74: | Line 77: | ||
===== Required Files ===== | ===== 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 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> | <code - mode1.inp> | ||
Line 121: | Line 129: | ||
| | ||
! 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 | ||
Line 254: | Line 262: | ||
<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 | ||
Line 492: | Line 505: | ||
<code - relaxed_slab.xyz> | <code - relaxed_slab.xyz> | ||
- | Ti -0.0303205158 | + | 108 |
- | O 0.4617571277 | + | |
- | Ti -1.3490231074 | + | Ti -0.0196732895 |
- | O -1.7878355710 | + | O 0.4723754303 |
- | O -3.1920046188 | + | Ti -1.3559074694 |
- | O -1.7392688578 | + | O -1.7917634261 |
- | Ti -3.7013678101 | + | O -3.2061730694 |
- | O 0.3820939857 | + | O -1.7223354624 |
- | Ti 3.7648454616 | + | Ti -3.7072315168 |
- | O 3.3744220782 | + | O 0.3901175533 |
- | O -4.6517384122 | + | Ti 3.7576915752 |
- | O -5.3048604582 | + | O 3.3911899157 |
- | Ti -0.0322712821 | + | O -4.6411313870 |
- | O 0.4616863664 | + | O -5.3047652050 |
- | Ti -1.3486854111 | + | Ti -0.0207144299 |
- | O -1.7878502749 | + | O 0.4723696865 |
- | O -3.1920078900 | + | Ti -1.3558005079 |
- | O -1.7391317134 | + | O -1.7918422000 |
- | Ti -3.7016680076 | + | O -3.2061826485 |
- | O 0.3819663832 | + | O -1.7223161680 |
- | Ti 3.7645108291 | + | Ti -3.7072713992 |
- | O 3.3742300683 | + | O 0.3900935320 |
- | O -4.6518683783 | + | Ti 3.7576114879 |
- | O -5.3048543483 | + | O 3.3911555573 |
- | Ti -0.0322471283 | + | O -4.6411391763 |
- | O 0.4616410032 | + | O -5.3047626840 |
- | Ti -1.3487988694 | + | Ti -0.0207062513 |
- | O -1.7878722642 | + | O 0.4723667071 |
- | O -3.1920029890 | + | Ti -1.3558175168 |
- | O -1.7392431026 | + | O -1.7918406363 |
- | Ti -3.7014193029 | + | O -3.2061760961 |
- | O 0.3819997133 | + | O -1.7223390903 |
- | Ti 3.7647483625 | + | Ti -3.7072222362 |
- | O 3.3742664872 | + | O 0.3900787901 |
- | O -4.6518133313 | + | Ti 3.7576703685 |
- | O -5.3048288292 | + | O 3.3911596509 |
- | Ti -1.5273352567 | + | O -4.6411291967 |
- | O -1.0884291790 | + | O -5.3047626859 |
- | Ti -2.8437250381 | + | Ti -1.5161932358 |
- | O -3.3377699606 | + | O -1.0530794682 |
- | O -4.7315575216 | + | Ti -2.8375929946 |
- | O -3.2582658881 | + | O -3.3233955054 |
- | Ti -5.1456170241 | + | O -4.7234020378 |
- | O -1.1370163008 | + | O -3.2337827875 |
- | Ti 2.2684272586 | + | Ti -5.1341235465 |
- | O 1.8549863841 | + | O -1.1292018546 |
- | O 4.0251492312 | + | Ti 2.2748016978 |
- | O 3.3256500472 | + | O 1.8795957531 |
- | Ti -1.5273925374 | + | O 4.0603419699 |
- | O -1.0884224454 | + | O 3.3216577066 |
- | Ti -2.8449459037 | + | Ti -1.5162127974 |
- | O -3.3378256175 | + | O -1.0531792321 |
- | O -4.7314704529 | + | Ti -2.8387264069 |
- | O -3.2583566629 | + | O -3.3234176494 |
- | Ti -5.1450467769 | + | O -4.7234014156 |
- | O -1.1370531089 | + | O -3.2338808261 |
- | Ti 2.2691513647 | + | Ti -5.1337085619 |
- | O 1.8552723808 | + | O -1.1292133652 |
- | O 4.0250669926 | + | Ti 2.2753347025 |
- | O 3.3256275888 | + | O 1.8797137276 |
- | Ti -1.5273691557 | + | O 4.0603607770 |
- | O -1.0883945790 | + | O 3.3216956874 |
- | Ti -2.8449849058 | + | Ti -1.5161826614 |
- | O -3.3378273935 | + | O -1.0531788180 |
- | O -4.7314320343 | + | Ti -2.8387418861 |
- | O -3.2583140921 | + | O -3.3234140545 |
- | Ti -5.1451041749 | + | O -4.7234083483 |
- | O -1.1370619143 | + | O -3.2338028141 |
- | Ti 2.2691991364 | + | Ti -5.1337579488 |
- | O 1.8552364131 | + | O -1.1292026624 |
- | O 4.0251145329 | + | Ti 2.2752985947 |
- | O 3.3256667516 | + | O 1.8797190226 |
- | Ti 1.4115723468 | + | O 4.0603653380 |
- | O -2.6848950906 | + | O 3.3217002712 |
- | Ti -4.2880054626 | + | Ti 1.4062179326 |
- | O -0.1913341931 | + | O -2.6647908793 |
- | O 3.9764368989 | + | Ti -4.2783192715 |
- | O -4.7977239298 | + | O -0.1912654580 |
- | Ti 3.5861119961 | + | O 3.9842928859 |
- | O 1.9214961536 | + | O -4.8135555127 |
- | Ti 0.8253184367 | + | Ti 3.5973231742 |
- | O 0.3158104050 | + | O 1.9073102520 |
- | O 2.4285293806 | + | Ti 0.8351562937 |
- | O 1.7757125179 | + | O 0.2999501886 |
- | Ti 1.4122145794 | + | O 2.4486923948 |
- | O -2.6849548157 | + | O 1.7901009453 |
- | Ti -4.2881462846 | + | Ti 1.4062978231 |
- | O -0.1913221230 | + | O -2.6648159269 |
- | O 3.9764565359 | + | Ti -4.2783858420 |
- | O -4.7977200607 | + | O -0.1912655926 |
- | Ti 3.5861498714 | + | O 3.9842992272 |
- | O 1.9214690372 | + | O -4.8135568089 |
- | Ti 0.8253871242 | + | Ti 3.5973007930 |
- | O 0.3157839337 | + | O 1.9073227407 |
- | O 2.4285525968 | + | Ti 0.8351415277 |
- | O 1.7756666228 | + | O 0.2999374565 |
- | Ti 1.4120341934 | + | O 2.4486955431 |
- | O -2.6849563408 | + | O 1.7900885384 |
- | Ti -4.2880783536 | + | Ti 1.4062636238 |
- | O -0.1913429323 | + | O -2.6648052713 |
- | O 3.9764639959 | + | Ti -4.2783535642 |
- | O -4.7976917037 | + | O -0.1912672794 |
- | Ti 3.5862152261 | + | O 3.9842996857 |
- | O 1.9214600134 | + | O -4.8135603835 |
- | Ti 0.8254109865 | + | Ti 3.5972989622 |
- | O 0.3157698685 | + | O 1.9073252382 |
- | O 2.4285566515 | + | Ti 0.8351502243 |
- | O 1.7757049357 | + | O 0.2999353645 |
+ | O 2.4486964067 | ||
+ | O 1.7900926030 | ||
</ | </ |
exercises/2014_ethz_mmm/dye_tio.1396600990.txt.gz · Last modified: 2020/08/21 10:14 (external edit)