dockonsurf / docs / source / about.rst @ 4fd2e6f0
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| 1 | 4fd2e6f0 | Carles Martí | About |
|---|---|---|---|
| 2 | 4fd2e6f0 | Carles Martí | ===== |
| 3 | 4fd2e6f0 | Carles Martí | |
| 4 | 4fd2e6f0 | Carles Martí | DockOnSurf is a program to automatically find the most stable geometry for molecules |
| 5 | 4fd2e6f0 | Carles Martí | on surfaces. |
| 6 | 4fd2e6f0 | Carles Martí | |
| 7 | 4fd2e6f0 | Carles Martí | webpage: https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf |
| 8 | 4fd2e6f0 | Carles Martí | |
| 9 | 4fd2e6f0 | Carles Martí | Features |
| 10 | 4fd2e6f0 | Carles Martí | ^^^^^^^^ |
| 11 | 4fd2e6f0 | Carles Martí | * Generate a handful of adsorbate-surface structures by |
| 12 | 4fd2e6f0 | Carles Martí | combining: |
| 13 | 4fd2e6f0 | Carles Martí | * surface sites |
| 14 | 4fd2e6f0 | Carles Martí | * adsorbate's anchoring points |
| 15 | 4fd2e6f0 | Carles Martí | * conformers |
| 16 | 4fd2e6f0 | Carles Martí | * orientations |
| 17 | 4fd2e6f0 | Carles Martí | * probe dissociation of acidic H |
| 18 | 4fd2e6f0 | Carles Martí | |
| 19 | 4fd2e6f0 | Carles Martí | * Guess the direction where to place the adsorbate. |
| 20 | 4fd2e6f0 | Carles Martí | Useful for nanoparticles or stepped/kinked surfaces. |
| 21 | 4fd2e6f0 | Carles Martí | |
| 22 | 4fd2e6f0 | Carles Martí | * Sample different orientations efficiently by using internal angles. |
| 23 | 4fd2e6f0 | Carles Martí | |
| 24 | 4fd2e6f0 | Carles Martí | * Detect and correct atomic clashes. |
| 25 | 4fd2e6f0 | Carles Martí | |
| 26 | 4fd2e6f0 | Carles Martí | * Optimize the geometry of the generated structures using CP2K or VASP. |
| 27 | 4fd2e6f0 | Carles Martí | |
| 28 | 4fd2e6f0 | Carles Martí | * Submit jobs to your computing center and check if they have finished normally. |
| 29 | 4fd2e6f0 | Carles Martí | |
| 30 | 4fd2e6f0 | Carles Martí | * Track progress by logging all events on a log file. |
| 31 | 4fd2e6f0 | Carles Martí | |
| 32 | 4fd2e6f0 | Carles Martí | * Customize the execution by changing chemically meaningful the edition of a simple input file. |