What you need to know about job talk (MIT OCW)?

I recently watched "How To Speak by Patrick Winston" from MIT OCW.  Thanks to Patrick Wilson who summarized everything you need to know when you are giving a talk which otherwise would take a complete course or at least 10 hours of lectures.

This 60 minutes talk provide you

1. Rules of Engagement @03:17
2. How to Start @04:20
3. Four Sample Heuristics @05:44
4. The Tools: Time and Place @10:23
5. The Tools: Boards, Props, and Slides @13:30
6. Informing: Promise, Inspiration, How to Think @36:35
7. Persuading: Oral Exams, Job Talks, Getting Famous @41:45
8. How to Stop: Final Slide, Final Words @53:15
9. Final Words: Joke, Thank You, Examples @56:40

In a job talk, Patrick Winston says (based on discussion with his colleagues) , the candidate should show

1. vision
2. done something
..
...
......
Conclusions by enumerating what you have done.


How to show that you have a vision?
You have to define the big problem and your approach to solve that big problem. He uses his field of interest "AI" to show the vision. How to understand human intelligence? What are the differences between Chimpanzee, Neanderthals  and Humans? Well. Human has the ability to grasp symbols and tell story based on a number of symbols by connecting them. How can I do to machines so that I could achieve the intelligence that human have in machines? That is an example for vision.

How to show that you have done something important?
List the number of steps you need to solve in order to solve the big problem (which you defined in your vision).
You can say "Here is what needs to be done". Specify some behavior, etc.

How to conclude your job talk?
You highlight what you have done so far and emphasize on where you are in achieving the big goal which you defined in your vision.

The transcript of the full talk (a 22 page pdf document) and the video can be accessed here.

English phrases for writing papers

Following list may be useful for writing papers, articles, etc.

"In recent years” vs “in the recent years”

Native speakers would generally prefer the second. The article is unnecessary and awkward. Both are correct. Personally, I find them all awkward and am much more likely to say things like "over the last few years" or just "recently".

Ref: https://english.stackexchange.com/a/59603/161843

Why you should learn Physics?

Why you should study Physics? Here is the answer from eminent people.

Elon Musk (SpaceX, Tesla, Boring Founder).

Physics gives you the way to think. There is something called "First principles" thinking where you don't assume anything and deconstruct very big problem (no matter how big it is) in to a smallest and simplest one. Elon Musk says in an interview that he use this first principles thinking to design rocket. He goes on, "What a rocket is made of?" A bunch of metals. What is the cost of those metals? About 2% of the total cost of the rocket. So, I can design a rocket at a much lower cost". 

Paul Graham (Y-Combinator)

Dr. Graham, a computer scientist (did PhD in computer science) gave a talk to aspiring entrepreneurs. What would you study in college (if a chance is given)? His answer is  

Best resources for Researchers

Lindau Nobel Laureate Meetings
Contain precious lectures given by prominent scientists

Web of Stories (YouTube Channel)
Contains memories of famous scientists told by themselves

What is your biggest lesson after publishing in Nature Journal?

"What is your biggest lesson?" This is the question that Nature asked researchers published in Nature recently.

Christina Hicks:
"I need to focus on myself for me. It’s easy to become really busy. I run up and down the mountains in the UK Lake District for fun. My brain gets cluttered and overworked if I don’t take a break. Running helps me to slow down."

Johan van den Hoogen:
"Working on that nematode paper helped me to appreciate the value of outsourcing — I didn’t develop the models in it. You should let other people do the things that they’re good at. I understand the models in the paper, but it would have taken me a year and half to create them on my own."

"My biggest realization is that you don’t need to move up the academic career ladder to have a satisfying career in science. The moment I stopped worrying about advancing in academia marked a change for me."

Stephanie Ellis:
"You have to have people around you who can point out the weaknesses in anything you do."

Oscar Serrano:
"Some relationships are more mutually beneficial than others. You can collaborate for years with someone and then realize it’s been a one-way street. You’re sharing ideas and resources with them but getting little in return. But other people really do give back as much as they get and really help you grow your career. I want to be the person that people want to collaborate with because it’s reciprocal."

Here is the full article from Nature.com

This is how a researcher actually develop a new method and what others think of it.

When a new method is developed, how different persons involved perceive the path of the research flow? Here it is.

How much is this true? Comment on this.

Credit: Facebook page Interesting Science.

configure, make, make install

Most of the linux/unix packages can be installed just by following three simple steps:

"configure, make and make install"

Try:

./configure
make
make install


If you are working in a cluster or workstation where you don't have sudo previleges, you just need to change the configure as follow. Remaining same.

Try:

./configure --prefix=/the/location/where/you/want/to/install/the/package
make
make install


Some codes use make -j . What is that?

Here is the explanation from "man" page of make.

-j [jobs], --jobs[=jobs]
"Specifies  the number of jobs (commands) to run simultaneously.  If there is more than one -j option, the last one is effective.  If the -j option is given without an argument, make will not limit the number of jobs that can run simultaneously."

Some other questions about make.

What is the difference between make and make all?

To List of things you need to work on HPC (for researchers)

For learning more, see
Make install but not to default directories
How to build: Configure and make

What are the types of book a researcher can write

Writing is a process of thinking and doing research. While writing research papers, a researcher undergoes a huge deal of reasoning, adding information, checking for clarity, checking for originality, checking for plagiarism, etc.

So, writing a book can solve this issue. 

What kind of book you may write? You may think

reference book

text book

monograph

But, here is the full list of type of books that you can write. 

1. almanac a book published every year that tells you about what happened in a particular subject or activity (note that this terminology is mostly used for astronomy. recently it is adopted for all fields)
2. annual a book or magazine published once every year
3. anthology a book containing poems, stories, or songs written by different people. Someone who produces an anthology is called an anthologist.
4. authority something such as a book that people respect because it contains a lot of knowledge about a particular subject
5. autobiography a book about your life that you write yourself
6. bible  a book that is considered the most important one for a particular subject
7. biography a book that someone writes about someone else’s life. 
8. booklet a small thin book that gives you information about something
9. catalogue a book , website or other resource containing pictures and information about things you can buy
10. coffee table book a large expensive book with a lot of pictures in it
11. collection poems, stories, or other pieces of writing that are published together in a book or on a website or other resource
12. companion used in the titles of books for showing that they are about a particular subject 
13. compendium formal a detailed collection of information on a particular subject, especially in a short book
14. cookbook a cookery book
15. cookery book british a book that contains recipes (=a list of the things you need and instructions for preparing and cooking food)
16. coursebook british a book that is designed to be used in class by students taking a particular course of study
17. dictionary a book, website or other resource which deals with a particular subject, providing the words, phrases, and terms used in that field, with information about their meaning and use
18. directory a book, website or other resource that lists information in alphabetical order
19. e-book or electronic book a book published on the Internet
20. encyclopedia a reference resource which provides information about many different subjects or about one particular subject. An encyclopedia may be published as a single book, a series of books, or as a digital product such as a website or an app.
21. folio a book made with very large pages
22. graded reader one of a series of books of various levels of difficulty containing pieces of writing, exercises etc, used by people who are learning to read or learning a language
23. grammar a book explaining the rules of a language
24. guide a book about a city, country, or area. This also means a book about a particular subject or type of activity
25. hagiography formal a book about a person’s life that deliberately includes only good things about them
26. handbook a small book that gives information about a subject or instructions about how to use something
27. hymnal a hymn book or a collection of hymns
28. instruction manual a book that tells you how to use a piece of equipment
29. literature books or other printed information about a subject
30. literature academic books and articles published about a particular subject
31. manual a book containing instructions for doing something, especially for operating a machine
32. memoir a written account of the life of someone who you knew well
33. memoirs an account of someone’s experiences written by that person, especially the experiences of someone who has taken part in important political or military events (academics too)
34. miscellany formal a book containing short pieces written by different people
35. monograph a formal piece of writing, or a short book on a particular subject
36. omnibus a book containing several stories that have already been printed separately
37. page-turner informal a book that is very interesting or exciting
38. pharmacopoeia a book, website or other resource that lists medicines and drugs used for treating medical conditions, and describes how to prepare and use them
39. picture book a book for children that consists mainly of pictures with little or no writing
40. presentation copy a copy of a book given to someone by the person who wrote or published it
41. primer a book that gives very simple instructions or basic information about something
42. prospectus a small book describing a school, university etc, and giving details of its courses
43. pullout a thin book that you can pull out of a magazine
44. quarto a book with pages that are quarto size
45. reader education a book containing simple pieces of writing, exercises etc, used by people who are learning to read or learning a language
46. reference book a book that is intended to be used when you need a fact or piece of information, for example a dictionary
47. rulebook a book that contains all the rules of an organization or a game
48. songbook a book that contains the words and music of a lot of songs
49. storybook a book containing one or more stories for children
50. symposium formal a collection of articles on a particular subject that are published together in a book
51. textbook or text a book containing information about one subject
52. thesaurus a book, website or other resource that contains lists of words that have similar meanings
53. title a book that is produced by a publisher
54. tome literary a large heavy book, usually about a serious subject
55. tutorial a book or a computer program that gives instructions on how to do something
56. yearbook a book containing pictures of people and details of the activities that they did at school or college during one particular year
57. yearbook american a book containing information about what happened in a particular business or community during a particular year

Google and Quantum Chemistry: Solving biggest problems in Quantum Chemistry

Google has just completed its first biggest quantum chemistry simulation ever. This is reported in a recent article from NewScientist (reference below, need subscription). Here, we provide our view on this recent news.

A few month back or so, Google announced its supremacy in Quantum Computing. Now, it has performed its first biggest quantum mechanical calculation using Quantum Computing.

Google's AI team works on quantum algorithms that can dramatically accelerate computational tasks for machine learning.

It is reported in NewScientist that long chain of hydrogen atoms has been studied using quantum computer developed by Google.

More info will be added soon....



References.

Read more: https://www.newscientist.com/article/2227244-google-has-performed-the-biggest-quantum-chemistry-simulation-ever/#ixzz67zVIhYdV

Learning resources from Standford

Resilience Stanford
Learning Connection
Stanford Online Courses (paid)
Coursera Courses from Stanford

(and more)

About Intel Compilers: What you need to know for computational scientists?

How to check Intel compiler versions?

icc --version
icc (ICC) 16.x.x.x
Copyright (C) 1985-2016 Intel Corporation.  All rights reserved.

icpc --version
icpc (ICC) 16.x.x.x
Copyright (C) 1985-2016 Intel Corporation.  All rights reserved.

ifort --version
ifort (IFORT) 16.x.x.x
Copyright (C) 1985-2016 Intel Corporation.  All rights reserved.

Working with MPI: Everything you need to know if you use HPC for science and engineering applications.

The usual questions for a beginner are.

What is MPI?
Why should we use it?
Is it a separate programming language compared to C/C++?
Is it compatible with Fortran/Python/C/C++?
What is the best language to learn MPI programming?
When do I need to use MPI programming?
What is "$PBS_O_DIR" and why should we use it in the script?
What are the commonly used tags in mpirun scripts?
What are some best practices of running MPI scripts?
What is a best program to illustrate the usefulness of MPI programming?
How to compile and run mpi program or script?
How to use laptop for dft or quantum chemistry or computational calculations?
How to compile and run mpi program or script in your laptop?
What is the difference or relation between qsub and MPI?

(add your questions. the questions will be answered one by one.)

Here I will discuss MPI and its usage in high performance computing for beginners in HPC usage.

How to know which version of MPI is installed in my cluster or supercomputer or system?

mpirun -version
You will get:
mpirun: IBM Platform MPI Community Edition: 09.x.x.x [BASELINE_MPI_POST_09xxxxx] [] Linux x86-64

How to check mpirun is successfully installed or not?

To check, simply check the version as above. In addition to that, you can run a simple program (C/C++, Fortran, or Python) that can tell you whether MPI is installed or not.

Now the simple program.

Here is a python program to check whether you have installed MPI or not (MPI Hello World program).

(if you get following error, you probably need to install the package.
"mpi_helloworld.c:10:17: fatal error: mpi.h: No such file or directory
compilation terminated."

(to be added more later)

Every compiler has an mpi version of it, usually with 'mpi' infront of it.

For example:

icpc - mpiicpc
g++ - mpig++
f90  - mpif90
f77  - mpif77
ifort - mpifort (note that one 'i' is missing here)

To run programs/codes compiled using these compilers, you need to use
"mpirun" command to run the jobs.

High performance computing using Cloud Computing: Where are we now?

I recently read an article in networkworld.com related to this topic.

The companies offer such solution is

IBM
AWS Amazon
Microsoft Azure

There is Google cloud. Does it offer similar solutions. Let us see later.

Almost all computational chemistry calculations and condensed matter theory calculations using density functional theory and other ab-initio and Monte-Carlo techniques use high performance computing (HPC) for computing. They are normally called as workstation, cluster, high performance computing, super computer, etc. These are used whenever time consuming calculations are need to be done as well as where there is a need for large memory. Large memory is needed for ab-initio calculations for storing the results such as the wave functions.

I wonder, is there any solutions where I can compile my code or commercial code or free code available on the internet such as Quantum Espresso in the cloud provides (see above in the list) and run these codes in the clouds?

My questions are:

How to use these clouds?
How much does it cost?
What is the comparison with HPC and Cloud computing?

I will post how I started using cloud computing for my high performance calculations.

How to search for a word in multiple PDF files in Linux

How to grep for a particular word in a PDF file?
Is it possible to use grep in pdf file?
How to use grep in pdf file?
Is there any command like grep to use in pdf files?

A simple solution exits. For all these questions, the answer is pdfgrep package.
There is a GitLab repository to do exactly this.

pdfgrep -R 'pattern' /path/of/the/pdf/file(s)

More on this:

See in more answers in StackOverflow 
Download the source from Gitlab 

A crash course on Fortran

Most of the condensed matter physics codes are written in Fortran and here is a quick summary of Fortran 95 language.

"

! To read a file.

    open(unit=11, file="records.txt", status="old") 
    ! The file is referred to by a 'unit number', an integer that you pick in
    ! the range 9:99. Status can be one of {'old','replace','new'}.
    read(unit=11, fmt="(3F10.2)") a, b, c
    close(11)

    ! To write a file.
    open(unit=12, file="records.txt", status="replace")
    write(12, "(F10.2,F10.2,F10.2)") c, b, a
    close(12)

"

References:
Learn Fortran95 in short duration

List of APIs useful for materials research

Materials Project
Nomad

How to unfollow the "New answer added to:" email from ResearchGate

I frequently get "New answer added to:" update to may email from ResearchGate. But, I don't want to get this update to my mail.

How to unsubscribe from this update to email.

You can do this as follow.

1. Go to the question. 
2. Below the questions there will be button "FOLLOW"
3. Click on the button once. 

That is it. You are done.

Adiabatic theorem and Born Oppenheimer Approximation

I try to understand the BO approximation here.

If we walk in mountain, some times, quit a bunch of mosquitoes like bees would fly around your head. You keep on hiking but the bees follow you by swirling around your head (and making noise too...really annoying).

Now, in molecule or materials, the nucleus can be given analogy of your head. The electrons can be given an analogy of bees around the head of a hiker. Here, the movement of the hiker's head (nucleus) does not affect the movement of bees (electron movement). This analogy may be useful for a kindergartner. But, for me, it is not enough. How to understand this really? Let us break this big problem in to pieces.

Another usual textbook discussion is the following. The mass of proton is 1837 times heavier than electron. Thus, nucleus is much much heavier than electron. Because of this, we can consider the nucleus is fixed in space and electrons are the only moving particles. This also doesn't makes sense to me. Just the higher mass consideration is not a satisfying argument to me.

So, I need a more intuitive as well as rigorous argument.

Let us start with Adiabatic theorem.

If a quantum system is changed gradually, the final state has the same state as the original state. Griffiths Quantum Mechanics beautifully explains this quantum adiabatic theorem. What if we change the system drastically?

Now, come to Born-Oppenheimer approximation. In BOA, we make use of this adiabatic theorem. Right? Where it is used? How it is used to prove it in original paper? Is there a simpler version (text book version) to understand the proof now?

Inserting symbols in MSWorld/PowerPoint

Many times, we may try to add an Angstrom (Å and also other symbols) symbol or degree celciums etc. But, we may need to search a lot in the insert Symbol option provided by MS Office (World and PowerPoint)

Here is the way how you can simply located those symbols.

Font: Select Normal Text
In the subset select Latin: Subset
You can find Angstrom symbol.

A straight forward way is copy the symbols here and paste in your document.

Character code is "00C5"

Hohenberg-Kohn theorems

I assume you know nothing about the Hohenberg-Kohn theorems. Here is the link for the paper that form the basis for the Kohn-Sham Density functional theory. Now, you download the paper and find skimming through the paper. You may not understand anything. Cool! It is not just you.

Here is a journey to understand Hohenberg-Kohn theorems.

The title is "Inhomogeneous electron gas". What we understand from this? We know electrons. What is electron gas? Collection of large number of electrons which behave like free electrons. Right?

Gas is defined as follow:
"a substance or matter in a state in which it will expand freely to fill the whole of a container, having no fixed shape (unlike a solid) and no fixed volume (unlike a liquid)."

Now, we may consider such gas which consist of electrons. However, materials have have nucleus which are positively charged and attract electrons and forms some weired kind of patterns/orbits/etc in the real materials. So, the electrons are not homogeneous inside a material and they must be in-homogeneous. Thus the title give some intuition on the subject of the paper.

Let us jump on the the formalism section.

First the authors start with the definition of the Hamiltonian and how it is actually written in different contributions added together.

H = T + U + V

Here, T, U and V stands for kinetic energy, electron-electron repulsion energy, and V is the electron-nucleus attractive potential energy.

List of Computational Physics and Computational Chemistry or Density Functional theory (DFT) Courses

Here is the list of Computational Physics and Computational Chemistry Courses that would be useful for learning and doing research in condensed matter physics or chemistry or biology.

LABORATORY OF COMPUTATIONAL PHYSICS (link here)
academic year 2015/16
Teacher: Maria Peressi

PY 502, Computational Physics, Fall 2018 (link here)
Department of Physics, Boston University
Instructor: Anders Sandvik

554027 Modern Fortran Programming for Chemists and Physicists (link here)
Trainer: Pekka Manninen

PhD Course and Lecture Series in Density Functional Theory  (link here)
Lecturer: Rickard Armiento, Linkoping University,

Materials simulations: Introduction to Density Functional Theory (2019) (link here)

Quantum Chemistry by Prof. Stephan P. A. Sauer (YouTube Videos Playlist)
Department of Chemistry, University of Copenhagen.

Summer Lecture Series in Theoretical Chemistry 2012: Density Functional Theory (YouTube link)
Prof. Sherrill, Georgia Institute of Technology.

Scientific Programming and Numerical Computation
from Wu-ting Tsai, National Taiwan University.