Unzip, Untar and unrar (of different extension)

To unzip file with an extension .Z (e.g. foo.Z)

gzip -d foo.Z

This will create a file name foo on the folder.

tar xvjf foo.tar.bz2

(here j uncompresses *.bz2 file)


To extract *.tar.xz file use xf parameters in command

$ tar xf file.tar.xz

Some files are compressed with .tgz (for example parallel_studio_xe_2017_update5_cluster_edition_online.tgz which is available as a free student edition from Intel).

tar -xvzf fftw-3.1.1.tar.gz  or tar -xvf fftw-3.1.1.tar.gz

We can use tar to extract a .tgz file.

tar -xvzf /path/to/yourfile.tgz

Here
x for extract
v for verbose
z for gnuzip
f for file (this 'f' should come last, just before the file name).

Similarly, for *.tar files,
tar -xvf fileName.tar

RAR Format

unrar e fileName.rar

This will extract all the files from .rar.

Relation between statistical adiabatic process and quantum adiabatic theorem

The adiabatic process which we learn in thermodynamics is the process where we decrease/increase the volume of the gases enclosed in a container, slowly so that the pressure remains constant throughout the process.

The quantum mechanical adiabatic theorem says: For a system with non-degenerate ground state, if the system is taken from the ground state to the next (only next excited state) energy level (i.e. excited state) very slowly (the time taken to go from one state to another in a smaller time than the characteristic time of the energy gap of the two energy-levels involved), then the system finally adapts ground state.

Here analogy is as follows (even though it doesn't make sense now)

• Which remains constant: Pressure & Energy
• Which is changed: Volume & State of the system
• In what time : Both are slowly (in QM, it is exactly defined; In TD, not defined (?) clearly.

Adiabatic theorem plays an important role in the definition of topological phases of matter.

In approximate (but most successful) theory such as Density Functional theory, construction of the final state is obtained by slowly changing some  parameters (for e.g., λ) and finally the ground state is obtained. 

What are the connection among these? 

Another similar idea (?) is the derivation of molecular forces by Feynman. What is the exact connection among these?

Topological Insulators

Recently, there is a widespread interest in the study of certain group of materials called "Topological Insulators" which may be considered as a subgroup of Quantum Materials.

First, what are topological materials?

Before coming to this question, we should know what is topology. I have been writing a separate post on Topology. Topology is a rich topic and consider spending a reasonable amount of time to get a clear picture of what really it is.

The 2016 Nobel prize has been awarded to David J. Thouless (University of Washington), F. Duncan M. Haldane (Princeton University) and J. Michael Kosterlitz (Brown University). The citation says that the prize is awarded "for theoretical discoveries of topological phase transitions and topological phases of matter".

To understand, let me give a rough idea. There are certain properties (eg. conductor on the surface only) which are protected in topological insulators. Here the word 'protected' means that the property won't vanish in any condition. You can do whatever modification you want i.e., you can change the sphere shaped material to any shape you want as for as you don't create edges/holes. If band structure is obtained for those different shapes, all other bands may change. But, surface states are protected and they will be always remain. When a hole is created in the material, these surface states will be destroyed. That is why, experts say that the property is "topologically protected".

These materials are interesting because of the technological applications and also many exotic phenomena they exhibit. 

1. Majorana Fermion
2. Weyl semi-metal
3. Dirac Fermion 
4. etc.

Following is a presentation by Prof. Charles Kane

Topological Band Theory I: Part 1 of 6.

Here is the part 2 of 6 videos:

Part 3 of 6:

Part 4 of 6:

Part 5 of 6:

Here is the final part of the presentation.

Spend as much time on understanding the materials presented in this video.

An introductory talk on the "Topological Insulators" from The Zurich Physics Colloquium given by Prof. Osterwalder Jürg would be useful.


(This page need additional improvement and update. Please visit this page later for a complete story. Comments are welcome. Thanks.)  

Accessing Ubuntu Bash files from Windows 10

How to access the files in the Ubuntu Bash update from the Windows 10.

The obvious way is through C:/ folder.

Here is the steps for doing that.

First you need to change the "Hidden folder" default option.

1. Open File Explorer
2. Select File --> Change folder and search options
3. Click on View tab, and select Show hidden files, folders, and drives (if already selected, leave as it is)
4. Click OK

Now, the hidden folders also will be visible. Remaining steps are

1. Click on the folder directory address box, copy and paste: %localappdata%\lxss and Enter
2. Now you will be in Bash directory: C:\Users\{username}\AppData\Local\lxss
3. Now you can access files in home folder and subfolders.

You can create a Shortcut to this folder (right click on home folder and select create shortcut) and paste the short cut in Desktop or convenient location quick access.

Windows PC Network disconnects after some time

Just chose "Never" in sleep mode.

This may solve the problem.

Notes on Relativity

Relativity theory (both special and general theories together) is considered to be one of the greatest intellectual marvels ever discovered by human. So to me no surprise why it is very hard to "really" understand and comprehend "Relativity theory". While special theory of relativity deals with the objects there are moving at constant speed (i.e., inertial motion only), general theory of relativity explores the difficult accelerating motions.

So, if you take long time to understand relativity theory, no worries. Just take a challenge and try to understand a little further.

OK. Before going to "What is" question, let us answer the question "Why".

When relativity is becomes important?

"Special relativity applies to situations where objects are moving very quickly, at speeds near the speed of light. Generally, one should account for relativistic effects when speeds are higher than 1/10th of the speed of light".

In graphene, relativistic effects are important because, the speed of electrons in graphene is of the order of c/300 (for reference see here)


Here is a list of questions you need Relativity to understand.



References

1. Special Relativity (see link: http://physics.bu.edu/py106/notes/Relativity.html)
2. Graphene: The running of the constants (http://www.nature.com/nphys/journal/v7/n9/full/nphys2066.html?message-global=remove)

Some other reading materials

What is the experimental basis of Special Relativity?

History of relativity (for Wikipedia)

Feynman's lectures on Special theory of relativity

Using Mendeley in a new PC

If you are using a PC for storing all the journal papers and now you want to change the PC, no worries. Follow these steps.

1.  Synchronize your files with the web.
2. Install Mendeley in new PC.
3. If you install and login, all of your papers will be downloaded in a single file or based on year (or whatever your settings is)
4. Copy the folder in which all of your files are stored and past in the new system where you want it
5. Again, upload from the new folder.
6. Now, go to the C:/Users/../Mendeley cut the folder and paste somewhere else (keep the file in case something goes wrong, you can again replace the file)
7. Now, if you open your file from Mendeley (using open the folder location), it will be linked to the desired folder.

Hope it helps. Comment if something is unclear.

How to do research Series (1/100)

Four golden lessons

by Prof. Steven Weinberg, Nobel Laureate in Physics (from Nature article)

Rule #1:

"I managed to get a quick PhD — though when I got it I knew almost nothing about physics. But I did learn one big thing: that no one knows everything, and you don't have to."


Rule #2:

"When I was teaching at the Massachusetts Institute of Technology in the late 1960s, a student told me that he wanted to go into general relativity rather than the area I was working on, elementary particle physics, because the principles of the former were well known, while the latter seemed like a mess to him. It struck me that he had just given a perfectly good reason for doing the opposite."

"My advice is to go for the messes — that's where the action is."

Rule #3:

It is to forgive yourself for wasting time. As you will never be sure which are the right problems to work on, most of the time that you spend in the laboratory or at your desk will be wasted. If you want to be creative, then you will have to get used to spending most of your time not being creative, to being becalmed on the ocean of scientific knowledge.

Rule #4:

Finally, learn something about the history of science, or at a minimum the history of your own branch of science. You can get great satisfaction by recognizing that your work in science is a part of history.

Reference:

These are extracted from: S. Wienberg, Scientist: Four golden lessons, Nature 426, 389 (27 November 2003) | doi:10.1038/426389a

Things to do when you leave your PC Series - Part 1

Now a days, it is normal to upgrade to a new PC. In older PC, we may use a lot of things such as synchronizing browsers, installing Dropbox etc.

• Before abandon old systems, these things have to be given much importance. The update link to such systems should be removed (especially for Dropbox etc).

• 
  
• Need to uninstall important personal packages. If some one is interested in a package, let them install the package again.

If you are using Mendeley, click here to read related to Medeley desktop.

(will be updated soon...)

Etymology of Scientific Words

convex

ˈkɒnvɛks/

adjective

adjective: convex

1. 1.

   having an outline or surface curved like the exterior of a circle or sphere.

   "a convex lens"

   synonyms:

   curved outwards, cambered; More

   antonyms:

   concave

2. 2.

   (of a polygon) not having any interior angles greater than 180°.

Origin

late 16th century: from Latin convexus ‘vaulted, arched’.

concave

ˈkɒnkeɪv/

adjective

adjective: concave

1. having an outline or surface that curves inwards like the interior of a circle or sphere.

   "concave lenses"

   synonyms:

   curved inwards, hollow, hollowed out, scooped out, depressed, sunken; More

   antonyms:

   convex

Origin

late Middle English: from Latin concavus, from con- ‘together’ + cavus ‘hollow’.

File name in Vim

When we are typing in Vim editor, often, we may want to see the file name.

This can be accomblished in following ways. After pressing ESC key

:f    
:file
ctrl + g

Hope it helps.


A related Q/A page can be seen in Stack Overflow page.

Using Ubuntu Software Center in Windows 10 Ubuntu Bash Terminal

As we know, Windows 10 has optional update for Ubuntu Bash.

But, after installing, it may be efficient if software center is used.

To check if package is available, type:

software-center --version

To open from terminal

software-center

To display a package detail 

software-center <packagename>

To install from terminal

sudo apt-get install software-cente

(approximately, 600 MB of packages will be downloaded and may take few minutes to 10 minutes)

Check if a Python module installed or not

For a beginner, it may be confusing whether a particular module in Python (either 2.* or 3.*). The simple way to check (in terminal is ) to import the module you want.

In the terminal, first go to python2 or python3 prompt. Then import the module you want to check. For example, if I you want to check if Numpy is installed or not, type "import numpy". If installed, the python interpreter will import. Otherwise, error message will be displayed.

Now example.

For python2, try:

~$ python     [in the terminal]
Python 2.7.12 (default, Oct  8 2019 time stamp)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy     [Enter]
>>>
Here note that you get a new >>> prompt and this means that numpy is already installed.

Now, I want to check a module called pythran is installed or not.

~$ python
Python 2.7.12 (default, Oct  8 2019, time stamp)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> pythran       [Enter]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'pythran' is not defined
>>>
This error means that this particular module is not installed.

We are here to help you what we learn. Comment here if you need any help on this or any question related to this post.

Making presentations that are friendly to colorblind people

Recently I stumbled upon excellent page with the following title:

How to make figures and presentations that are friendly to colorblind people, by Masataka Okabe, Jikei Medial School (Japan) and Kei Ito, University of Tokyo, Institute for Molecular and Cellular Biosciences (Japan)

3(+1) principles of Color Universal Design

1. Choose color schemes that can be easily identified by people with all types of color vision, in consideration with the actual lighting conditions and usage environment.
2. Use not only different colors but also a combination of different shapes, positions, line types and coloring patterns, to ensure that information is conveyed to all users including those who cannot distinguish differences in color.
3. Clearly state color names where users are expected to use color names in communication.
4. Moreover, aim for visually friendly and beautiful designs.

Click here for more tips to prepare god visual presentations.

Google Scholar (Research Tools Series 02)

As we know, Google Scholar has become an important part of researchers. Its algorithm captures the citations even from conference papers and Google Scholar is keep on improving.

Now Google Scholar has been updated and has a new look.

1. One can follow the Researchers for new articles and new citations for the researcher. 
2. One can obtain notification for new articles and citations.
3. One can add the co-authors
4. Can include the filed of expertise

Set an alias (Linux Tutorial Series 02)

Some times, setting alias may save a lot of time.

Setting alias is very simple.

1. Go to your home folder
2. Open .bashrc file with vim or other editors (vim .bashrc and enter)
3. At the end of the file, type:       alias vi='vim'
4. Exit the editor after saving
5. On the terminal, type: source .bashrc (enter)

Now your alias is set.

To see the list of alias in your system, type at the terminal: alias

This will list all the alias.


Here is some useful aliases.


alias grep='grep --color'
alias l.='ls -d .* --color=auto'
alias ll='ls -l --color=auto'
alias ls='ls --color=auto'
alias vi='vim'

You can comment on more useful aliases.

Here is another useful tip on alias.

In the above example, if you type 'ls', it will execute 'ls --color=auto'
However, sometime you may want to use unaliased 'ls'. This can be performed by using

backslash + comment.

Example.
\ls will execute just ls.

Hope this is useful.

Restricted or Unrestricted Calculations - Which one I should use?

Restricted calculation use single orbital for a pair of electrons. One electron with up and another electron with down spin occupy the same orbital. In unrestricted calculations, each electron occupy different orbital.

Okay. Which one to use for the calculations?

Generally, default formalism for closed-shell system is restricted calculation and the for the open-shell molecule, default calculation is unrestricted.

But, it is essential to do unrestricted calculations on closed-shell calculations also to confirm the ground state. For radicals (diradicals and polyradicals), it is essential to use both restricted and unrestricted calculations.

The restricted and unrestricted calculations should yield the same energy which implies there no symmetry breaking occur in those system.

The typical example for a molecule with triplet ground state is Oxygen molecule.

Read more on the following links:

• Understanding restricted vs unrestricted calculations

Women Scientists in Theoretical/Computational Chemistry

Recently found an interesting page which list Eminent Women Scientists who work on Theoretical/Computational Chemistry, Materials Science, etc.

The link for the list is here: Women Scientists.


This project is funded by the National Science Foundation. Content by Prof. Anna I. Krylov, University of Southern California.

What does "sudo dpkg" mean?

Many times, I have used following comment.

sudo dpkg link/to/the/package

But, what does that mean?

1. dpkg is the software at the base of the package management system in the free operating system Debian and its derivatives. 
2. dpkg can be used to install, remove, and provide information about .deb packages. 
3. dpkg (Debian Package) itself is a low level tool.

Moving from 32-bit OS to 64-bit OS does not affect you as you think...

For long time, I hesitated to update from 32-bit version to 64-version, because, I have some important packages (32-bit) which necessary for my tasks.

Recently, I understood that a 32-bit version can be installed in 64-bit OS also. So, now I am updating both my Linux and Windows OSs to 64-bit version.

I will update  my experience later.

Tools for a Scientific Code Developer

Through reading, I understand that following skills are essential for a researcher who write code.

Apart from a good command in Linux OS and bash scripting, I understand that coding ability using following languages is essential.

1. Python 
2. C and C++
3. Fortran

Following sites are useful

Stackexchange 

        In this site, I like Academia, StackOverflow, Unix & Linux etc. The good aspect I like is that you will get excellent answers.

GitHub Repository   

          One can use this site for version control of the code development.


Regular Expression 

       Regular expression is a key skill for a programmer. This regexr.com https://regexr.com/ provides a userfriendly plaform to learn and build REGEX expressions.

Vim Usage (Linux Tutorial Series - 01)

Vim Usage

Here I describe simple comments related to "vim" editor and its efficient usage.

To start to edit the the file

        vim foo.txt

(I have set an alias for vim as follow: vi='vim'. Because of this alias i can use just "vi" instead of typing "vim". To learn on how to set alias, see this page of the blog)

This will open the file foo.txt if file exist. If the file does not exist, it will open an empty file with the name foo.txt.
To start edit, press 'i' character (which means insert mode)
Now, you are ready to add text and edit the text.


After completing the edit, press 'ESC' key and press ":" and then type 'wq'. This will write and quit the file.

These are the basics in Vim.

I have set alias vi="vim" so that I can can use vi instead of vim.

Now to use Vim efficiently, I use navigation commands often (these also very basic too).

To move line by line (ESC mode).

    k – move upwards

    j – move downwards

    l – move right side

    h – move left side

To move to the particluar line (nth line in ESC mode):

    10k - move 10 line upwards
    10j - move 10 lines downwards
    NG - Go to the Nth line of the file.
    G  - Go to the end of the file.
    gg  - Go to the beginning of the file.


Navigation in a line (ESC mode)

    e – go to the end of the current word.
    b – go to the previous (before) word.
    w – go to the next word.


To navigate through paragraph:

    { – go to the beginning of the current paragraph (press '{' key again to move to previous paragrph) 
    } – go to the end of the current paragraph (press '}' again to move to the end of the next paragraph)

To Search:

    /i – to search the patter (will find the next occurence.)
    * – to go to the next occurrence of the current word under the cursor.

Navigation from Command Line

    vim +N file.txt     - open file.txt and go to the Nth line
    vim +/pattern file.txt - open the file and find the first occurenc of the pattern.


To delete lines (in ESC mode)":

dd - delete the current line
u - undo 

Move to the next/previous black line: Use } and { to move between black lines.

To delete the rest of the line (after the cursor)
Shift + d (or d$)



Delete till a word or character
d/<word>  will do the job.
For example, if I want to delete until the world "end", I would type

:d/end

This would delete all the words/line until the word "end".


If this page is useful, please comment.
You can give your suggestions too to improve the blog.