exercises:2014_ethz_mmm:dye_tio
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exercise:dye_tio [2014/04/04 11:14] – sclelia | 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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What you get should look similar to this: | What you get should look similar to this: | ||
- | {{ :exercise:dye_tio_bonding_density.png? | + | {{ dye_tio_bonding_density.png? |
===== 3. Task: Bonding energies | ===== 3. Task: Bonding energies | ||
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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 [[wp> | + | The provided [[wp> |
</ | </ | ||
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<code - mode2.xyz> | <code - mode2.xyz> | ||
116 | 116 | ||
- | |||
- | |||
Ti 0.0150786099 | Ti 0.0150786099 | ||
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108 | 108 | ||
- | Ti -0.0196732895 | + | Ti |
- | O | + | O |
- | | + | Ti |
- | O -1.7917634261 | + | O -1.7917634261 |
- | O -3.2061730694 | + | O -3.2061730694 |
- | O -1.7223354624 | + | O -1.7223354624 |
- | | + | Ti |
- | O | + | O |
- | | + | Ti 3.7576915752 |
- | O | + | O |
- | O -4.6411313870 | + | O -4.6411313870 |
- | O -5.3047652050 | + | O -5.3047652050 |
- | | + | Ti |
- | O | + | O |
- | | + | Ti |
- | O -1.7918422000 | + | O -1.7918422000 |
- | O -3.2061826485 | + | O -3.2061826485 |
- | O -1.7223161680 | + | O -1.7223161680 |
- | | + | Ti |
- | O | + | O |
- | | + | Ti 3.7576114879 |
- | O | + | O |
- | O -4.6411391763 | + | O -4.6411391763 |
- | O -5.3047626840 | + | O -5.3047626840 |
- | | + | Ti |
- | O | + | O |
- | | + | Ti |
- | O -1.7918406363 | + | O -1.7918406363 |
- | O -3.2061760961 | + | O -3.2061760961 |
- | O -1.7223390903 | + | O -1.7223390903 |
- | | + | Ti |
- | O | + | O |
- | | + | Ti 3.7576703685 |
- | O | + | O |
- | O -4.6411291967 | + | O -4.6411291967 |
- | O -5.3047626859 | + | O -5.3047626859 |
- | | + | Ti |
- | O -1.0530794682 | + | O -1.0530794682 |
- | | + | Ti |
- | O -3.3233955054 | + | O -3.3233955054 |
- | O -4.7234020378 | + | O -4.7234020378 |
- | O -3.2337827875 | + | O -3.2337827875 |
- | | + | Ti |
- | O -1.1292018546 | + | O -1.1292018546 |
- | | + | Ti 2.2748016978 |
- | O | + | O |
- | O | + | O |
- | O | + | O |
- | | + | Ti |
- | O -1.0531792321 | + | O -1.0531792321 |
- | | + | Ti |
- | O -3.3234176494 | + | O -3.3234176494 |
- | O -4.7234014156 | + | O -4.7234014156 |
- | O -3.2338808261 | + | O -3.2338808261 |
- | | + | Ti |
- | O -1.1292133652 | + | O -1.1292133652 |
- | | + | Ti 2.2753347025 |
- | O | + | O |
- | O | + | O |
- | O | + | O |
- | | + | Ti |
- | O -1.0531788180 | + | O -1.0531788180 |
- | | + | Ti |
- | O -3.3234140545 | + | O -3.3234140545 |
- | O -4.7234083483 | + | O -4.7234083483 |
- | O -3.2338028141 | + | O -3.2338028141 |
- | | + | Ti |
- | O -1.1292026624 | + | O -1.1292026624 |
- | | + | Ti 2.2752985947 |
- | O | + | O |
- | O | + | O |
- | O | + | O |
- | | + | Ti 1.4062179326 |
- | O -2.6647908793 | + | O -2.6647908793 |
- | | + | Ti |
- | O -0.1912654580 | + | O -0.1912654580 |
- | O | + | O |
- | O -4.8135555127 | + | O -4.8135555127 |
- | | + | Ti 3.5973231742 |
- | O | + | O |
- | | + | Ti 0.8351562937 |
- | O | + | O |
- | O | + | O |
- | O | + | O |
- | | + | Ti 1.4062978231 |
- | O -2.6648159269 | + | O -2.6648159269 |
- | | + | Ti |
- | O -0.1912655926 | + | O -0.1912655926 |
- | O | + | O |
- | O -4.8135568089 | + | O -4.8135568089 |
- | | + | Ti 3.5973007930 |
- | O | + | O |
- | | + | Ti 0.8351415277 |
- | O | + | O |
- | O | + | O |
- | O | + | O |
- | | + | Ti 1.4062636238 |
- | O -2.6648052713 | + | O -2.6648052713 |
- | | + | Ti |
- | O -0.1912672794 | + | O -0.1912672794 |
- | O | + | O |
- | O -4.8135603835 | + | O -4.8135603835 |
- | | + | Ti 3.5972989622 |
- | O | + | O |
- | | + | Ti 0.8351502243 |
- | O | + | O |
- | O | + | O |
- | O | + | O |
</ | </ |
exercises/2014_ethz_mmm/dye_tio.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1