exercises:2014_ethz_mmm:dye_tio
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exercise:dye_tio [2014/04/04 09:19] – [2. Task: Bond induced density differences] 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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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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<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 - mode1.xyz> | <code - mode1.xyz> | ||
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+ | |||
+ | </ | ||
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+ | <code - mode2.xyz> | ||
116 | 116 | ||
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H -1.3211320733 | H -1.3211320733 | ||
C -2.2774669737 | C -2.2774669737 | ||
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H -0.3897742635 | H -0.3897742635 | ||
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</ | </ | ||
<code - relaxed_slab.xyz> | <code - relaxed_slab.xyz> | ||
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</ | </ |
exercises/2014_ethz_mmm/dye_tio.1396603198.txt.gz · Last modified: 2020/08/21 10:14 (external edit)