PyCon APAC 2022|一般演講 Talks|國泰金控 Cathay Financial Holdings / 美光科技 Micron 冠名贊助
✏️ 共筆 Note:https://hackmd.io/@pycontw/rJ9-wp7Js
?? Slido:https://app.sli.do/event/vfJvpCnMQH1ymLxcfcgbxZ
? 語言 Language:英文 English
? 層級 Level:中階 Intermediate
? 分類 Category:科學 Science
? 摘要 Abstract ?
Molecular Dynamics (MD) is a powerful numerical technique to predict the behavior of atoms and complex materials without a full quantum mechanical treatment. It makes it much faster to do simulation/optimization for a wide range of sciences and technologies, from designing new drugs and genetic treatments of disease to nano- & next-gen semiconductor materials to industrial chemical & semiconductor processing to fundamental surface sciences. In this talk I’ll first explain the basics in an easy-to-understand way and run some pure python “DIY” implementations so we can see “under the hood” what’s going on. Then I’ll introduce LAMMPS via Python and associated packages, build some molecular structures, evolve them dynamically and see the results in 3D. https://www.lammps.org/pictures.html#lammpspaper You’ll understand the basics and be able to install LAMMPS and start simple MD calculations right away, then refer to the tutorials and examples provided at the end of the talk.
? 說明 Description ?
Molecular Dynamics (MD) is a powerful simulation/optimization tool for a wide range of sciences and technologies from designing new drugs and genetic treatments of disease to nano- & next-gen semiconductor materials to industrial chemical & semiconductor processing to fundamental surface sciences.
MD allows us to calculate/predict how molecules move, interact & form new structures and to realistically optimize these processes theoretically using a mix of basic physics (ball-and-spring models) and just enough quantum mechanics to get the job done. Sounds complicated but the basic idea is still pretty simple to understand.
We’ll first run simple Python scripts that use SciPy & NumPy to build multi-atomic systems and let them move to find their minimum energy configuration comparing minimizers scipy.optimize.minimize and scipy.optimize.dual_annealing. Then we’ll do true dynamical calculations using scipy.integrate.solve_ivp and the FIRE[1, 2] algorithm. We’ll look at how to move this calculation to GPU via CuPy[3].
Then we’ll move to a big, full-blown calculation using very popular and flexible program LAMMPS[4-7] (now thankfully wrapped in friendly and easy-to-use Python wrapper) and some “helper” packages and the many open-source force-field options - the models for the way atoms interact. We’ll run through several well-documented examples and see what resources are available for further study.
[1] FIRE: “Structural Relaxation Made Simple” Bitzek et al. (2006) Phys. Rev. Lett. 97, 170201
[2] http://users.jyu.fi/~pekkosk/resources/pdf/FIRE.pdf
[3] CuPy: https://cupy.dev/
[4] https://en.wikipedia.org/wiki/LAMMPS
[5] https://www.lammps.org/
[6] “LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales” https://doi.org/10.1016/j.cpc.2021.108171
[7] Cool Pictures from LAMMPS Simulations https://www.lammps.org/pictures.html#lammpspaper
? 講者介紹 About Speaker - David Mikolas ?
[0, None, False. np.nan]
#pycontw #pyconapac2022 #python #moleculardynamics #science #lammps
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https://www.youtube.com/watch?v=zgytV3Kb8lM
Day 2, 11:30-12:00
Abstract
Imagine you are a data engineer and in charge of a data pipeline. What do you think is the most important thing for the data pipeline? I think it is definitely the quality of data! However, the more complex your data pipeline becomes, the harder it is to maintain the data quality. For example, what if the format of some source data is changed without being noticed? What if some program update includes a bug? Such things cause data issues. It can take a long time to find the issues. Or even worse, your stakeholders may find the issues before you do! Great Expectations helps you solve such problems. It is a Python-based open-source library for validating, documenting, and profiling your data. It allows you to define the shape of data, test data, and document the results. In this talk, I will introduce you Great Expectations and share my experience with it. Let's make your data pipeline robust with Great Expectations!
Description
Great Expectations A Python-based open-source library for validating, documenting, and profiling your data.
Slides: https://docs.google.com/presentation/d/1ttwYJdFYLT9x87fusVAPBgcxZpEAE3g7AZ5eic34I7s/edit#slide=id.p
HackMD: https://hackmd.io/@pycontw/2021/%2F%40pycontw%2FHJRVK7qMt
Speaker: Keisuke Nishitani
A data engineer and python programmer in Osaka, Japan. Working on a data pipeline built on Amazon Redshift, Amazon S3 and AWS Lambda. Interested in data workflow frameworks, data analysis and data visualization.
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https://www.youtube.com/watch?v=e8XhXG-NiWk
Day 2, 10:00-11:20
Abstract
Storing data in a tabular format is not always ideal. Taking advantage of strong data in knowledge graphs can make handling complex data structure possible and data visualization easier. In this workshop, you will get all the basics to start modelling data in the terms of triples and building schemas of a knowledge graph.
Description
Short Format of your Workshop
Overview-5 min, Lecture - 30 mins, Breaks- 10 minutes, Hands-on training - 40 mins, Closing - 5 mins
Course Benefits
You will have learnt a new skill set that may assist you in your project in data science or research. You will have a new tool that you can better model your data and collaborate with others. Also, you gain all the prerequisites to use WOQL - a query language for knowledge graph and the TerminusDB Python client to manage, manipulate and visualize data in your knowledge graph.
What is required from attendees
A computer with stable internet connection; TerminusDB Desktop App or Docker image (a.k.a TerminusDB Bootstrap) which you can download from https://terminusdb.com/hub/download (FREE); Python client for TerminusDB (require Python equal or larger than 3.6); An opened mind and ready to learn something new
Slides: https://terminusdb.com/blog/
HackMD: https://hackmd.io/@pycontw/2021/%2F%40pycontw%2FBkR6iXczF
Speaker: Cheuk Ting Ho
Cheuk has been a Data Scientist in various companies which demands high numerical and programmatical skills, especially in Python. To follow her passion for the tech community, now Cheuk is the Developer Relations Lead at TerminusDB - an open-source graph database. Cheuk maintains its Python client and engages with its user community daily. Besides her work, Cheuk enjoys talking about Python in personal streaming platform and MidMeetPy podcast. Cheuk has also been a guest speaker at Universities and various conferences. On top of speaking at conferences, Cheuk also participates as organizers. Conferences that Cheuk has organized include EuroPython(which she is a board member of), PyData Global and Pyjamas Conf. Believing in gender equality, Cheuk constantly organizes workshops and mentored sprints to support Tech Diversity and Inclusion.
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https://www.youtube.com/watch?v=2agT-LLKVYw
Speaker: Tzung-Bi Shih
ZoneIDAProc provides an easy way to export Linux proc-like interface for python program. It is intuitive and convenient for showing process internal data; even expose a complex computation. The talk focuses on demonstrating the magic of ZoneIDA and how it increases your program's versatility.
About the speaker
Tzung-Bi Shih was born in Xi-Hu, Taiwan, in 1988. He received Bachelor and M.S. degree in Computer Science from National Chiao Tung University in 2010 and 2011, respectively. He was a R&D engineer in Trend Micro during 2011-2014.
He has been a Python programmer for 2 years. He is a beginning researcher and he is interested in operating system, computer architecture, especially, in parallel computing.
組織/公司 Independent
https://tw.pycon.org/2015apac/zh/program/53
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https://www.youtube.com/watch?v=2Nwa-I_F-d0