dockonsurf / docs / source / index.rst @ 0969983f
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| 1 | 4fd2e6f0 | Carles Martí | .. DockOnSurf documentation master file, created by |
|---|---|---|---|
| 2 | 4fd2e6f0 | Carles Martí | sphinx-quickstart on Thu Feb 11 20:09:40 2021. |
| 3 | 4fd2e6f0 | Carles Martí | You can adapt this file completely to your liking, but it should at least |
| 4 | 4fd2e6f0 | Carles Martí | contain the root `toctree` directive. |
| 5 | 4fd2e6f0 | Carles Martí | |
| 6 | 4fd2e6f0 | Carles Martí | DockOnSurf |
| 7 | 4fd2e6f0 | Carles Martí | ========== |
| 8 | 4fd2e6f0 | Carles Martí | |
| 9 | f6624e99 | Carles Martí | DockOnSurf is a program to automatically find the most stable geometry for |
| 10 | f6624e99 | Carles Martí | molecules on surfaces. |
| 11 | 4fd2e6f0 | Carles Martí | |
| 12 | 4fd2e6f0 | Carles Martí | Features |
| 13 | 4fd2e6f0 | Carles Martí | ^^^^^^^^ |
| 14 | 4fd2e6f0 | Carles Martí | * Generate a handful of adsorbate-surface structures by combining: |
| 15 | 4fd2e6f0 | Carles Martí | |
| 16 | 4fd2e6f0 | Carles Martí | * surface sites |
| 17 | 4fd2e6f0 | Carles Martí | * adsorbate's anchoring points |
| 18 | 4fd2e6f0 | Carles Martí | * conformers |
| 19 | 4fd2e6f0 | Carles Martí | * orientations |
| 20 | 4fd2e6f0 | Carles Martí | * probe dissociation of acidic H |
| 21 | 4fd2e6f0 | Carles Martí | |
| 22 | f6624e99 | Carles Martí | * Guess the direction where to place the adsorbate. Useful for nanoparticles or |
| 23 | f6624e99 | Carles Martí | stepped/kinked surfaces. |
| 24 | 4fd2e6f0 | Carles Martí | |
| 25 | 4fd2e6f0 | Carles Martí | * Sample different orientations efficiently by using internal angles. |
| 26 | 4fd2e6f0 | Carles Martí | |
| 27 | 4fd2e6f0 | Carles Martí | * Detect and correct atomic clashes. |
| 28 | 4fd2e6f0 | Carles Martí | |
| 29 | 4fd2e6f0 | Carles Martí | * Optimize the geometry of the generated structures using CP2K or VASP. |
| 30 | 4fd2e6f0 | Carles Martí | |
| 31 | 4fd2e6f0 | Carles Martí | * Submit jobs to your computing center and check if they have finished normally. |
| 32 | 4fd2e6f0 | Carles Martí | |
| 33 | 4fd2e6f0 | Carles Martí | * Track progress by logging all events on a log file. |
| 34 | 4fd2e6f0 | Carles Martí | |
| 35 | f6624e99 | Carles Martí | * Customize the execution by changing chemically meaningful the edition of a |
| 36 | f6624e99 | Carles Martí | simple input file. DockOnSurf is a program to automatically find the most |
| 37 | f6624e99 | Carles Martí | stable geometry for molecules on surfaces. |
| 38 | 4fd2e6f0 | Carles Martí | |
| 39 | 4fd2e6f0 | Carles Martí | |
| 40 | 4fd2e6f0 | Carles Martí | .. toctree:: |
| 41 | 4fd2e6f0 | Carles Martí | :maxdepth: 2 |
| 42 | 4fd2e6f0 | Carles Martí | :caption: Contents |
| 43 | 4fd2e6f0 | Carles Martí | |
| 44 | 4fd2e6f0 | Carles Martí | about |
| 45 | 4fd2e6f0 | Carles Martí | installation |
| 46 | 4fd2e6f0 | Carles Martí | tutorials |
| 47 | 4fd2e6f0 | Carles Martí | inp_ref_manual |
| 48 | 4fd2e6f0 | Carles Martí | tips_and_tricks |
| 49 | 4fd2e6f0 | Carles Martí | faqs |
| 50 | 4fd2e6f0 | Carles Martí | release_notes |
| 51 | 4fd2e6f0 | Carles Martí | contact |
| 52 | 4fd2e6f0 | Carles Martí | license |
| 53 | 4fd2e6f0 | Carles Martí | |
| 54 | 4fd2e6f0 | Carles Martí | |
| 55 | 4fd2e6f0 | Carles Martí | |
| 56 | 4fd2e6f0 | Carles Martí | Indices and tables |
| 57 | 4fd2e6f0 | Carles Martí | ================== |
| 58 | 4fd2e6f0 | Carles Martí | |
| 59 | 4fd2e6f0 | Carles Martí | * :ref:`genindex` |
| 60 | 4fd2e6f0 | Carles Martí | * :ref:`modindex` |
| 61 | 4fd2e6f0 | Carles Martí | * :ref:`search` |