replacing the example / recipes with a tutorial page and improvements #148
Conversation
andrewtarzia
left a comment
andrewtarzia
left a comment
There was a problem hiding this comment.
Looking very good!
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
Co-authored-by: Andrew Tarzia <andrew.tarzia@gmail.com>
| streamline the analysis of many-body trajectories, offering a consistent and | ||
| user-friendly interface across most analysis tasks. | ||
|
|
||
| This is achieved through the classe, :class:`.trajectory.Trj`, which corresponds to an |
There was a problem hiding this comment.
"class" invece di "classe"
matteobecchi
left a comment
matteobecchi
left a comment
There was a problem hiding this comment.
Very nice! Definitely better organized than before.
| Now the ``trj`` variable contains the trajectory, and using the methods of the | ||
| :class:`.trajectory.Trj` class we can perform all the dynsight analyses on | ||
| this trajectory. For instance, let's say we want to compute the LENS | ||
| descriptor (`published paper <https://doi.org/10.1073/pnas.2300565120>`__). |
There was a problem hiding this comment.
Since in the nex tutorial TimeSOAP is cited as Caruso et al., here it is better to cite lens as "Crippa et al." and not as "published paper"
|
|
||
| The :class:`.trajectory.Insight` objects can directly be used to perform post-processing such as smoothing (see the other `tutorials pages <../tutorials_menu.html>`_). | ||
| But they can also be used to perform clustering analysis. In this example, we will show how to use the | ||
| ``Onion Clustering`` method (`published paper <https://doi.org/10.1073/pnas.2403771121>`__) to cluster the LENS values computed above. |
There was a problem hiding this comment.
Also here, cite it as Becchi et al.
|
|
||
| In this tutorial, we will show you the effect of noise reduction by using | ||
| the spatial denoising algorithm implemented in ``dynsight`` (Related paper: `Donkor et al. <https://doi.org/10.1021/acs.jpclett.4c00383>`__, `Martino et al. <https://doi.org/10.1088/2632-2153/adfa66>`__). | ||
| We will also explain a new application of the Onion Clustering algorithm to explore different time resolutions for the classification (:class:`.trajectory.Insight.get_onion_analysis()`). |
There was a problem hiding this comment.
maybe is not "a new application of Onion Clustering", but "another application of Onion Clustering"
ChiaraLionello
left a comment
ChiaraLionello
left a comment
There was a problem hiding this comment.
I think now they are very clear and I like how they are organized. Good job!
andrewtarzia
left a comment
andrewtarzia
left a comment
There was a problem hiding this comment.
Looks good! Some comments still to do, and we discussed using doctests in the examples still.
| topo_file=files_path / "ice_water_ox.gro", | ||
| ) | ||
| In this tutorial, we will use the descriptor ``TimeSOAP`` ( `Caruso et al. <https://doi.org/10.1063/5.0147025>`__). |
There was a problem hiding this comment.
remove space before Caruso
| time window the one that corresponds to the highest number of clusters and longest ``delta_t`` (in this case, ``delta_t=37`` frames). | ||
| This choice should guarantee that the clusters identified are stable for longer time. | ||
|
|
||
| .. code-block:: python |
There was a problem hiding this comment.
Use the same "new line" or "one line" formatting for all, this looks messy
| _, tsoap = trj.get_timesoap( | ||
| soap_insight=soap, | ||
| ) | ||
| """ |
There was a problem hiding this comment.
remove this comment, in my opinion
| n_jobs=4, # Adjust n_jobs according to your computer capabilities | ||
| ) | ||
| the ``soap`` variable is a :class:`.trajectory.Insight` object that contains the computed ``SOAP`` spectra. |
| examples/info_gain/trj_*.npy | ||
| tests/systems/coex/.* | ||
| tests/systems/.* | ||
| .DS_Store |
There was a problem hiding this comment.
just delete these off your computer?
There was a problem hiding this comment.
It's macOS; every mac user will have this annoying and useless DS_Store. I would ignore it.
If it's a problem, i'll remove that line
4 participants
hi all;
Just revising the example creating step by step tutorial (GROMACS style)
not finish yet but at least you can have a look.
PS -> there is the possbility to find some "flying" files here and there; don't worry i will clean everything.