Intro to the Linux
Shiferaw G.
PhD, Assistant Prof.
Introduction
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An operating system
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Developed at Bell Labs in the 1960’s
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Command Line Interpreter
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GUIs (Window systems) are now available
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Linux is free
➢ It’s fully customizable
➢ It’s stable (i.e. it almost never crashes)
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These characteristics make it an ideal OS for programmers and
scientists
mkdir
mkdir is used to create new directories. For example
try:
mkdir diamond to make a directory called
'diamond'.
pwd-print working directory
To orient yourself, type pwd.
This shows the folder (directory) you are in.
ls
ls is the command used to list the contents of a directory. Contents can be files and other directories.
cd
cd is used to change directory.
You can specify either the full path, or the directory you want to go to as a relative path, in relation to
your current working directory.
rm
• rm is used to delete files. For example:
• touch test-file makes a file called 'test-file'.
• type ls -lh to examine the new file.
• Type rm test-file to delete, and ls -lh to check it was
deleted.
• rm alone will delete files but not folders. To delete a
folder, use
• rm -r to delete recursively. However be careful with rm -r,
because if you delete a root directory containing
• the rest of your filesystem, it will be gone.
cp
• cp is used to copy files, as cp sourcefile newfile.
For example:
• make a file with touch important-file.
• copy it, cp test-file another test2-file.
To copy a file another location, specify the relative path like
• cp test2-file some-relative-path/another test2-file
• To copy a folder, use the recursive option, cp -r sourcedirectory newdirectory.
mv
• mv is used to move files or directories from one location to another. It is also useful to rename files
and folders.
Try moving location by:
• typing mv another-important-file ../. to move the file one level up.
• typing mv ../another-important-file . to move it back.
DFT calculations with Quantum Espresso
• Important QE input and output.
• Converge essential calculation parameters such as planewaves and k-point sampling.
• Compute interatomic forces, and determine lattice parameters by minimising the crystal total energy.
• Compute electronic properties band structure , Dos
• Compute bulk modulus, thermodynamic ppts
QE IO
There are three mandatory NAMELISTS in PWscf:
&CONTROL
input variables that control the flux of the calculation and the amount of
I/O on disk and on the screen.
&SYSTEM
input variables that specify the system under study.
&ELECTRONS
input variables that control the algorithms used to reach the self-consistent
solution of KS equations for the electrons.
There are three additional NAMELISTS in PWscf that must be specified
under certain circumstances:
&IONS
needed when ATOMS MOVE! IGNORED otherwise ! input variables that
control ionic motion in molecular dynamics run or structural relaxation
&CELL
needed when CELL MOVES! IGNORED otherwise ! input variables that
control the cell-shape evolution in a variable-cell-shape MD or structural
relaxation
&EE
needed when density counter charge corrections are used to solve the problem
with open boundary conditions
ATOMIC_SPECIES
name, mass and pseudopotential used for each atomic species present in the
system
ATOMIC_POSITIONS
type and coordinates of each atom in the unit cell
K_POINTS
coordinates and weights of the k-points used for BZ integration
There are additional INPUT CARDS in PWscf that must be specified
only under certain circumstances.
CELL_PARAMETERS
OCCUPATIONS
Plane‐wave cut‐off energy
The controllable parameter to test the convergence is the cut‐off energy related to
how many plane waves are used in the calculation. The large numbers of plane waves
give a better result through the memory and CPU time increase with increasing the
cut‐off energy. In this tutorial, we show how to select a suitable value of the cut‐off
energy.
In Quantum ESPRESSO, the electronic wavefunction is represented by the linear
combination of plane waves, where the maximum value of G max is related to the cut‐
off energy E cut‐off = h2/2m Gmax2 Ry (1 Ry = 13.6 eV). We will change the value of
the cut‐off energy from 5 to 50 Ry to check the convergence of total energy in this
tutorial.
k‐points for Brillouin‐zone integration
Other controllable parameter to test for convergence of the total energy is k‐points grid.
The integration on k in the Brillouin zone (BZ) is approximated by summation of finite
numbers of k‐ points that is called k‐points grid. In this tutorial, we show how to select
the k‐points grid.
In Quantum ESPRESSO, there are six values to determine a k‐points grid, in which the
first three values are set as the number of k‐points mesh of each axis, and the last three
values are a parameter to move the lattice of each axis. The total number of k‐points is
obtained by multiplying the first three values. For example, k1 , k 2 , and k3 are set to 10,
10, and 1, respectively, then the total number of k‐points is 10 × 10 × 1 = 100.
Optimizing equilibrium Lattice constant
