Hi Ujjwal],
please see my comments within your e-mail.
Best regards,
Nikos
Στις 27/3/2023 12:37 μ.μ., ο/η Ujjwal Shekhar έγραψε:
Greetings,
I hope you are doing well. Thank you for taking the time to review my
work and providing feedback. I have created a Pull Request
<https://github.com/nixeimar/Apothesis/pull/23> on GitHub to add the
parametric study's Python scripts. The commit message outlines my plan
for cleaning the codebase and improving the usability of the added
feature and details the changes I have made so far and the TO-DOs for
further improvement. Should I create a different folder, titled
"examples", and add a "parametric study" folder inside it with a
README.md detailing how to use it?
*_Commit message_*
Added Python scripts to do a parametric study test
TODOS:
- Arrange in a separate folder.
- Refactor into a single script.
- Add README for parametric_study
*Yes please do do. **
*
I have started working on the proposal. I am currently following the
Proposal Template
<https://ellak.gr/wiki/index.php?title=Proposal_Template> provided by
GFOSS. However, the website has some outdated information, so I listed
a few doubts I had:
* In the *Basic Details *section, it asks for my "_IRC nickname on
#sugar"._ Does GFOSS have an IRC channel that I can join?
* In the *Your Motivation *section, it asks, "_Why did you choose
Sugar Labs ?_" Is this a typo? Should I replace "Sugar Labs" with
"GFOSS"?
* In the *Motivation * section (at the end of the template). It asks
for the following: _Convince us that you will be a good fit for
the GFOSS project you have selected by sharing links from GFOSS
Projects._ However, the link attached is the following (Click Here
<https://ellak.gr/wiki/index.php?title=Google_Summer_of_Code_2019_proposed_ideas>).
This has a list of GSoC projects from 2019. What should I fill in
here?
*No you should not do anything from the above. Sugar Labs is the project
so I assume it means Apothesis. **
*
I also had a few doubts regarding the content that I am adding in my
proposal:
* I have also attached a few research articles demonstrating the
importance of implementing HCP and Diamond Lattices in Apothesis
in my proposal. Are there any resources/ scholarly articles you
suggest I use to grasp the underlying concepts better?
*What you have added are sufficient. **
*
* For the*Timeline*section, I would like to ask for guidance. What
is the best approach, or do you have a tentative timeline? I would
appreciate your input.
*If your proposal is successful, the timeline is 12 weeks (3 months).
One month per lattice and one month for preparation/validation would be
great. **
*
*
* Should I also add a section detailing my educational background in
the *Previous Work *section?
*Yes, this could be very useful. **
*
I have attached a draft of my proposal for your review, I will be done
with all sections except for the *Milestones *and*Timeline *section,
which I will start working on soon. I appreciate any feedback or
criticism you might have. I am looking forward to hearing back from you.
*Up till now it looks great! **
*
Best Regards,
Ujjwal Shekhar **
------------------------------------------------------------------------
*From:* Nikolaos (Nikos) Cheimarios <nixeimar [ at ] chemeng [ dot ] ntua [ dot ] gr>
*Sent:* Saturday, March 25, 2023 1:05 PM
*To:* Ujjwal Shekhar <ujjwal [ dot ] shekhar [ at ] research [ dot ] iiit [ dot ] ac [ dot ] in>;
gsoc-developers [ at ] ellak [ dot ] gr <gsoc-developers [ at ] ellak [ dot ] gr>
*Subject:* Re: GSoC Project - Interest in "Creating new lattices for
Apothesis" idea
Hi Ujjwal,
nice work!
I am not sure about the python scripts, since the main idea is that
the user will only use the input file which is a plain text.
However, it is really we can have it on apothesis for someone that
would like to use it.
Yes please, go ahead and create the PR.
And yes please also start working on your proposal and when you have a
finished draft I can take a look and provide feedback.
Best regards,
Nikos
Στις 24/3/2023 7:43 π.μ., ο/η Ujjwal Shekhar έγραψε:
Greetings,
I hope this message finds you well.
Over the past day, I have been working on Apothesis and have made
some progress in tweaking input.kmc to achieve different runs. I have
created several Python scripts to run Apothesis with different input
parameters and have also written two additional scripts to clean the
outputs and generate plots. Please find attached the scripts, the
results obtained, and a few inferences.
I have identified a few potential Quality of Life improvements,
including adding details on how to run the software in the README.md,
moving the ./apothesis executable inside the src folder, and
providing instructions on how to use the attached script(s) in the
PDF. Should I make pull requests for the first two, since they are
essential to anyone using Apothesis?
Moving forward, I would appreciate your guidance on what steps to
take next. Should I begin working on my proposal? If so, what
components should I include, and do you think I should update you at
certain intervals?
Please let me know your thoughts and any feedback or criticism you
may have. Thank you for your valuable time and consideration.
Best regards,
Ujjwal Shekhar
------------------------------------------------------------------------
*From:* Nikolaos (Nikos) Cheimarios <nixeimar [ at ] chemeng [ dot ] ntua [ dot ] gr>
<mailto:nixeimar [ at ] chemeng [ dot ] ntua [ dot ] gr>
*Sent:* Wednesday, March 22, 2023 8:38 PM
*To:* Ujjwal Shekhar <ujjwal [ dot ] shekhar [ at ] research [ dot ] iiit [ dot ] ac [ dot ] in>
<mailto:ujjwal [ dot ] shekhar [ at ] research [ dot ] iiit [ dot ] ac [ dot ] in>; gsoc-developers [ at ] ellak [ dot ] gr
<mailto:gsoc-developers [ at ] ellak [ dot ] gr> <gsoc-developers [ at ] ellak [ dot ] gr>
<mailto:gsoc-developers [ at ] ellak [ dot ] gr>
*Subject:* Re: GSoC Project - Interest in "Creating new lattices for
Apothesis" idea
Τhank you very much Ujjwal.
You have done an excellent work.
I kindly ask you to perform some experiments with Apothesis.
The input file contains the system to simulate.
CO + * -> CO*: constant 0.4 #0.389
This is the yCO.
O2 + 2* -> 2O*: constant 0.15 all #0.611
This is the yO.
I kindly ask you to make a parametric study, i.e. change the value of
yCO from 0.1 to 0.9 and yO = (1-yCO)/4
and measure the growth rate and the coverage.
Set time to 1000 (e.g. time: 1000).
So at the end you can report a table:
time step | yCO | yO | growth rate | coverage CO | coverage O |
The time step in the table is where the run will stop. Once you
execute apothesis you will understand what I am talking about.
Best regards,
Nikos
Στις 22/3/2023 12:55 μ.μ., ο/η Ujjwal Shekhar έγραψε:
Greetings,
I hope you're doing well. I have successfully compiled Apothesis on
my local machine and have attached the commands I used for future
reference.
Furthermore, I have been actively working on expanding my
understanding of Monte Carlo methods and basic Markov Chains beyond
the scope of my coursework. Yesterday, I studied these concepts from
various online resources and specifically explored how to model
Graphene lattice using KMC. Although the resource used MATLAB, I am
confident that I can easily replicate the concepts in C++. I have
included my notes and relevant links for you to look over.
Moving forward, I would appreciate your guidance on what steps to
take next. Should I begin working on my proposal? If so, what
components should I include, and do you think I should update you at
certain intervals? I welcome any feedback or criticism that you may
have.
Thank you for your valuable time and consideration.
Best regards,
Ujjwal Shekhar
/P.S.: The commands used for compiling Apothesis on Ubuntu 20.02
```bash (In the Apothesis directory)
/
/sudo apt install qtchooser/
/sudo apt-get install qt5-default/
/qmake/
/make
```/
_
_
------------------------------------------------------------------------
*From:* Nikolaos (Nikos) Cheimarios <nixeimar [ at ] chemeng [ dot ] ntua [ dot ] gr>
<mailto:nixeimar [ at ] chemeng [ dot ] ntua [ dot ] gr>
*Sent:* Tuesday, March 21, 2023 2:06 PM
*To:* gsoc-developers [ at ] ellak [ dot ] gr <mailto:gsoc-developers [ at ] ellak [ dot ] gr>
<gsoc-developers [ at ] ellak [ dot ] gr> <mailto:gsoc-developers [ at ] ellak [ dot ] gr>; Ujjwal
Shekhar <ujjwal [ dot ] shekhar [ at ] research [ dot ] iiit [ dot ] ac [ dot ] in>
<mailto:ujjwal [ dot ] shekhar [ at ] research [ dot ] iiit [ dot ] ac [ dot ] in>
*Subject:* GSoC Project - Interest in "Creating new lattices for
Apothesis" idea
Dear Ujjwal. Thank you for you interest in our project.
I kindly ask you to first compile apothesis.
Are you familiar with the kinetic Monte Carlo method?
Best regards,
Nikos
----
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