Linux tips: Run new command with previous arguments

Tip 2:

type history.

All of your recent commands would be listed.

12 ls
13 sudo make && make install
14 cd ~/myapps/

Here, if you want to install the 13nth command (i.e., sudo make && make install)

Use as follow
!13

This will run the 13th command.


Tip 3:

Use ctrl + R to reverse search the history and type any part of the command.
For example, in the above case, if you press ctrl+R and then type sudo, the command "sudo make && make install" will be displayed.
If you want to run that command, press Enter.
Otherwise, presss ctrl+R till you get the relevent command.
If you dont't want to run anything, press ctrl+C.


Here is text.

To use previous argument (only one argument present)

$_ or !$

For example, vi ~/home/application/readme
Now, if you want to cat the file,
you can use
cat !$Where there are many arguments, you can handle like following. ls file1.txt file2.txt and you wanted the first one, you could type !:1 giving file1.txt If you want to use both arguments !:1-2 This will list both files file1.txt and file2.txt You can use any argument by mentioning the number of the argument as fillow !:20-34 !:1-3 To run new command with all the arguments !:^-$

Extract only the number from a file name

Some times you may want to extract only the number from a file name, especially when you are working with a huge number of files to do some calculation or to run jobs.

This can be done by (for foo_bar_xyz_file_01_input.in)

echo $f|cut -d_ -f5

Here, $f is the file name.
-d is the delimeter
-f5 is the field where the number is present.

Check compiler versions

For any compiler or application, to check the version, just use '''-V" to check the version.

ifort -V

Linux Tips - Reverse search (ctrl +R)

To reverse search the history of commands you used, you can use Ctrl+R and then type any part of the command. For example,

configure && make && make install

Here, if you want to execute this commands again (after several commands)

Just type ctrl+R and type make

If not displayed, type ctrl+R again.

Once your command is displayed, type Enter.

To cancel the suggested command, type ctrl+C (as usually done in Linux terminal)

Suppose, you type the command history and want a slight modification in the 250th command.

!250:p 

If you want to run a command similar to 250th command, but want to modify before running that command, use this format. This will print the command. Then, using up arrow key, you can edit the command and re-run. 

Combining PDF - the easiest way in Linux

To combine two or more .PDF files, one can use "pdfunite" application, which is installed in Ubuntu Linux by default.

To combine n number of files,

pdfunite file1.pdf file2.pdf file3.pdf outfile.pdf

Running  this command will combine all the files in to the outfile named outfile.pdf.

Setting path (How to do it)

Setting path is one of the most encountered problem for a beginner in Linux. Setting path is very simple.

To see what are present in the current path, type

echo $PATH echo$LD_LIBRARY_PATH

To list these as a list

echo "${PATH//:/$'\n'}" echo "${LD_LIBRARY_PATH//:/$'\n'}"

Now, come to our aim.

Go the the directory, where your directory is.

Type pwd to print the current working directory.

Now insert following line in .bashrc (or .profile) file

export PATH=$PATH:/path/to/dir

then

source ~/.bashrc

Schroedinger's equation

The famous theoretician Paul Dirac wrote in his paper published in 1929 as follows:

"The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation." (6 April 1929)

(to see a completely different perspective, read more is different by the theoretician P W Anderson "More is Different" article published in Science Magazine.


Schrodinger's equation is the equation of motion for the matter waves. Now, what is matter waves? Waves associated with the matter particles (eg. electron, proton, ect) are called matter waves. So, the equation of matter waves will describe the entire property of the matter waves. The solution to this wave equation will give you a function that is called "wave function". Wave function itself is a complex entity. It has been very difficult to define the meaning of the wave function. However, the square of the wave function (the product of the complex conjugate and the wave function which is termed as the probability density) gives the probability of finding the particle at a given location at a given time. Note that, the wave function does not have any interpretation, whereas its square has the physical interpretation. 

Why do we need Schrodinger's equation?

Can we describe the entire universe with Schrodinger's equation?
In principle, yes. The former director of the Perimeter Institue Niel Turok gave a fantastic public lecture on the topic "The Astonishing Simplicity of Everything". Watch the full talk here.

If we solve the Schrodinger's equation, we can get the wave function (solution to the Schrodinger's equation). In principle, this wave function contain all information about the system of interest. Note that to for the equation, we need the potential acting on the system/electron/particle.

The realistic problem that we can use Schrodinger's equation to solve is the hydrogen (or hydrogen-like atoms He+, Li2+, Be3+, B4+, C5+ ) atom where there is only one electron. We can solve the Schrodinger's equation for atoms (or molecules or solids) having more than one electron (not even He) accurately. This is technically named as analytical solution is not possible (or too difficult to solve). But, we need solution (we need wave function to calculate the properties of the atom/molecules/solids). Here comes the approximation techniques. We can use approximation techniques to solve Schrodinger's equation and get the properties that we are interested in.

The textbook problems we learn using Schrodinger's equation are:

1. Free particle (potential=0)
2. Potential step
3. Finite potential well
4. Infinite potential well
5. Tunneling through the barrier
6. Particle in a 1D box (linear molecules)
7. Particle in a 3D box
8. Simple harmonic motion
9. Hydrogen atom model

A crucial development in this field is the formulation of Hohenberg-Kohn theorems. There are two theorems. These theorems the basis for the formulation of Kohn-Sham Density functional theory (see here in other post on this topic and in Wikipedia).

The Kohn-Sham density functional theory for which Walter Kohn (and John A Pople) has been awarded is based on those theorems. We saw that on solving the Schrodinger's equation, we get wave function. From this wave function, we can get the properties of the system (atom/molecule/solid). However, HK theorems proves that the density (which is a physical quantity and can be observed) is a fundamental variable from which we can get the energy (and hence all other properties).

Suppose we have N number of electrons in the system. The KS-DFT formalism reduces a complex N-electron problem in to N number of 1-electron Schrodinger-like equation. Note that we writ Schrodinger-like equation. Yes. Why? Because, we replace the actual potential in Schrodinger equation with an effective potential in KS-DFT. Wonderful. Right? But wait.

This simplification comes with a trouble (???). There is an important ingredient (exchange and correlation functional) which has been proven to exist but nobody (to this day) knows its mathematical form. The exchange and correlation functional is approximated and calculations are performed to predict the properties of materials (from gas to liquid to solids). Generally it works and give good results. However, many problems remain and these problems are attributed to the approximation of the important ingredient. To know more about the theory, see this post on "Density Functional Theory".

Hyperwebster: A dictionary made of infinite words and all of the texts, poems, everything written and ye to writeen (Paradoxes series #1)

If we create words from the alpaphet A....Z , like

A

AA

AAA.......A

B

BB

BBB........B

.

.

.

Z

ZZ

ZZZ........Z

Then, 

AB

AAB

...

AAA.....B

and then finally

.

.

.

......Z

If we create such words, this dictionary would contain everything written so far and future words, books, all of the text-worlds.

A mind blowing idea.

(need update)

Check R is installed or not

To check whether R is installed or not, type

$R

or type

$which R

or you can use

$type R

List of numerical libraries used in Quantum Chemistry / Computational Materials Science codes

The speed of a quantum chemical calculation often depends on how efficient the used numerical libraries are. Here is a list of numerical libraries that are widely used in various scientific codes.

C Program based
FFTW
GNU Scientific Libarary
Intel MKL (includes BLAS, LAPACK, ScaLAPACK, FFT, etc)

C++ Program based
Armadillo
LAPACK++
Intel MKL

Fortran Program based
LAPACK
LINPACK
Netlib

Python Program based
NumPy
SciPy
ScientificPython
SymPy