Apparently this was stuck in my drafts folder
On Fri, Mar 9, 2018 at 7:30 AM, B Adarsh <badar...@gmail.com> wrote:
> Including support for Quantum Espresso with Avogadro is not quite an
> idealistic thing to do at the moment, as it will have the same problem as
> faced by VASP, i.e. apart from the positions of the various atomic species,
> one also needs to provide a couple of other details like energy cutoffs,
> pesudopotentials etc in the same input file, unlike other popular packages
> where there is a standalone file for atomic positions. I can definitely try
> to come up with a way to tackle that, starting with setting default values
> for some of those unknown parameters, but yeah I would like to have ideas
> and opinions heard on the same.
>
> Meanwhile, I have been fixing minor bugs I have been coming across in
> Avogadro, and that has also given me the chance to look and examine through
> various scripts. And since I have about two weeks before the proposal
> deadline, I would like to get more information on the plan to include
> support for MD.
>
> 1. I guess we would be starting with parsing the output files of the
> MD calculations and getting details of each time step. First ideas that
> struck my mind were along the lines of including a slider for navigating to
> the n'th timestep (or playing the time step evolution as an animation), so
> that one can visualize how the atoms move along each time step.
>
> This is already present, although it needs improvement. It features some
basics for XYZ files moving through trajectory steps in the player tool.
>
> 1. Focusing on the reading of large files is an interesting aspect to
> explore, both algorithmically and through code. I shall read more about
> some of the common encoding techniques and try to investigate whether
> techniques for time series analysis like data differencing, can help get
> better insights on the data we have.
> 2. Once the major backbone is dealt with, focusing on
> cross-compatibility with various MD codes is to be explored. Whether
> following JSON setup similar to the one already existing for the core
> framework, or adopting some other writing techniques, is to be explored
> too.
>
> I would like to know the ideas and plan of action you have in mind for the
> project. This will help me frame a structured timeline for the proposal.
> Also, I would like to know whether you are comfortable with having a look
> at proposal drafts before the official submission deadline.
> Looking forward to your reply.
>
Happy to look at drafts. LAMMPS and GROMACS would be two of the main open
source MD codes, but there are many others, the ideas page mentions quite a
few of them. We are looking for someone who can figure out the best way of
reading output from these codes, look at efficient methods of reading the
trajectory, even generate input for some of these codes.
Beyond that there is a need to generate data about changes, highlighting
where atoms are most active for example, maybe processing the trajectory
file and tracing out the lines of movement, or linking an energy-time graph
with the 3D view. To an extent this is up to you as a student to research
needs in this area, and I am happy to provide feedback on ideas. You should
scope something that is reasonably ambitious, yet realistic. Your goals,
and milestones are used to assess the success of the project.
Thanks,
Marcus
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