materials square

Exclusive Tutorial by Dr.Mosab Banisalman

Contents

A DFT Intro

B Input File

C Adsorption & DOS

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A DFT Intro

First Principle (ab-initio) method for electrons

Density Functional Theory Computational Quantum Chemistry

Electron density Wave function

Kohn-Sham eq. Schrödinger eq.

Solids Molecules
Physics, MSE Chemistry

Chemistry (1998)
• DFT is a quantum mechanical method used to investigate
the electronic structure of many-body systems • Study systems at the quantum level. It encompasses a
• Instead of focusing on wavefunctions, DFT deals with wide variety of methods, including DFT, Hartree-Fock,
electron densities, which reduces the computational post-Hartree-Fock methods
problem significantly • Codes used: Gaussian, ORCA, GAMESS, MOLPRO, Q-
4
• DFT relies on the Kohn-Sham method Chem, NWChem, etc
• Codes used: Quantum ESPRESSO, VASP, SIESTA, GPAW, • Molecular systems.
CASTEP, and many others.
• Studying solid materials.
A DFT Intro

Schrodinger equation

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A DFT Intro

What is DFT?
• Definition: Density Functional Theory (DFT) is a quantum mechanical method used
to study molecular and solid-state electronic systems.
• Core Idea: Instead of solving the complex many-body Schrödinger equation directly,
DFT focuses on the electron density as the primary variable.

• Why hard: 1 H (1 electron and 1 proton , then this is 6 coordinates) and then we have
6 degree of freedom (DOF). If it is O = 48 DOF

• In Schrodinger equation complexity doesn't add up it multiplies. 6

• In DFT we don’t care about quantum state of system, but we care (and we aim to find)
electron density of that system.
• Its Like predict how noisy the classroom rather than predicting every kids' movement.
A DFT Intro

Why use DFT?

•Accuracy: Provides a good balance between computational efficiency and
accuracy.
•Flexibility: Can be applied to a wide range of systems – atoms, molecules, and
solids.
•Cost-effective: Less computationally intensive than other quantum mechanical
methods, like Hartree-Fock (Approximate the wavefunction of a multi-electron system
by considering electron-electron interactions in an averaged manner.) and post-Hartree-
Fock (Include the electron correlation missed in the basic Hartree-Fock method).
DFT (Instead of working directly with the many-electron wavefunction (as in HF), DFT
works with the electron density, a simpler entity.)

•Comparison: Unlike Molecular Dynamics (MD) which focuses on atomic

movements, DFT offers insights into electronic structures and properties.
7
A DFT Intro

Why use DFT?

•Biochemistry: Understanding
enzyme-substrate interactions or
drug binding affinities.
•Surface Science: Investigating the
adsorption of molecules on metal
surfaces.
•Catalysts: Designing more efficient
catalysts for chemical reactions, like
hydrogen production.
•Batteries: Studying ion migration
in battery electrodes to improve 8

energy storage.
MDPI image
A DFT Intro

Why use DFT?

•Memory Systems: Exploring
magnetic or ferroelectric properties
essential for memory devices.
•Mechanical Characteristics:
Predicting the strength and elasticity
of new materials.
•Photonics: Designing materials
with specific optical properties for
telecommunications or imaging.

MDPI image
A DFT Intro

Strengths and weakness of DFT?

Good For:
•Density of States (DOS): Accurately describes the electronic state distribution over
energy.
•Structure Determination: Predicts equilibrium geometries and atomic arrangements
effectively.
•Vibrational Frequencies: Good for predicting vibrational modes of molecules and
materials.

Might not be good for:

•Band Gaps: Often underestimates band gaps in semiconductors. This is because
standard DFT, using approximations like LDA or GGA, does not capture the correct
long-range electron-electron correlations.
•Dispersion Interactions: Struggles with long-range van der Waals interactions
without specific corrections.
•Strongly Correlated Systems: Has challenges with systems where electron-electron
10
interactions are strong, like in some transition metal oxides.
A DFT Intro

Key Concepts & Potentials

1.PAW (Projected Augmented Wave):
1. Aspect: Describes the treatment of electron-ion interactions in DFT
calculations.
2. Purpose: PAW is a method to efficiently handle the electronic structure near
atomic cores, combining the accuracy of all-electron calculations with the
efficiency of pseudopotentials.

2.LDA (Local Density Approximation) and GGA (Generalized Gradient

Approximation):
1. Aspect: Describes the treatment of electron-electron interactions, specifically
the exchange-correlation energy in DFT calculations.
2. Purpose: The exact form of the exchange-correlation energy is not known. LDA
and GGA are two different approximations to tackle this problem.
1. LDA: Considers the electron density at a point in space and uses a uniform
electron gas approximation to estimate the exchange-correlation energy.
2. GGA: Improves upon LDA by considering not only the electron density but
also its gradients (i.e., how the density varies in space). This often provides a
more accurate description for many systems.
 materials square Materials Square Education

Quantum Espresso Input File

12
B Input File

Chemical Energy and Post-processing of SCF

Contents
1 Input File
• &CONTROL
• &SYSTEM
• &ELECTRON
• K_POINTS
• ATOMIC_SPECIES
• ATOMIC_POSITION

13
B Input File

The DFT calculation progress

Convergence Test (K-Points + Energy Cut-off)

Structure Relaxation

Self-Consistent Filed Find Physical properties (band ,

Calculation (SCF) optical, E ,etc)

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•

•
• Introduction
• Paragraph 1
Paragraph 2
• Paragraph 3
• Paragraph 4
Summary
•
•
•
• Namelists , end with /

•
•
•
•
• &Control
------------ name card 1
• ------------ name card 2
.
• /
• New

•
•
•
•
•
•
•
•
 What type of
• calculation we
want to apply
•
•
•
•
•
 Pseudopotential
• directory
(path location)
•
•
•
•
•
•
•
•
pseudo_dir = '/home/user/pseudopotentials’,
• pseudo_dir = ‘.’
•
•
 Pseudopotential
• directory
(path location)
•
• Name cards: Calculations, pseudo_dir,
• prefix, outdir, etc.
•
•
•
• &System
------------ name card 1
• ------------ name card 2
• .
/
• New
•
 geometry of the
• system
•
•
• Ecutrho = 220

• Smearing=‘f-d’

•
 geometry of the
• system
•
•
• Ecutrho = 220

• Smearing=‘f-d’

•
 Number of
• atoms in
• supercell

•
• Ecutrho = 220

• Smearing=‘f-d’

•
• Types of atoms
presented
• H2O(2 types)
•
• Ecutrho = 220

• Smearing=‘f-d’

•
•
Energy cutoff
• wavefunctions
(Ry) unit
•
• Ecutrho = 220

• Smearing=‘f-d’

•
•
• Energy cutoff
wavefunctions
• (Ry) unit
• Ecutrho = 220

• Smearing=‘f-d’

•
•
•
• Used to improve
the convergence
• Ecutrho = 220

• Smearing=‘f-d’

• smearing = 'gaussian'
smearing = 'methfessel-paxton'
smearing = 'marzari-vanderbilt'
smearing = 'fermi-dirac’
•
• &ELECTRON
------------
• ------------
• /
New
•
•
•
• Max number of
• &Electron
Electron_maxstep=200
iterations in one
scf
• Conv_thr= 0.000001
Startingpot=atomic

•
•
•
•
Desired
• &Electron
Electron_maxstep=200
accuracy
• Conv_thr= 0.000001
Startingpot=atomic

•
•
•
•
• &Electron
Electron_maxstep=200
Starting
potential
• Conv_thr= 0.000001
Startingpot=atomic

•
• Startingpot=file
'charge-density.xml':
•
•
•
• K-POINTS
• (not a namlist)

•
•
•
•
sets the
• sampling of the
• Brillouin zone

• •
•
•
•
•
•
•
• •
•
•
•
•
•
•
• ATOMIC_SPECIES
(not a namlist)
•
•
•
•
•
•
Type, coordinates
• of each atom in
unit cell.
•
Barriers Barrier 1 Equipments

Expensive Equipment
High Performance Computer (HPC)
At least $200K + Maintenance

Physical Background
Barrier 2
Physical Background
Should be know computational physics
More than 1yr

Linux Environment

Barrier 3
TOO MANY BARRIERS !! Complex Linux environment
Linux command, w/o GUI
materials square
Adsorption Energy
Adsorption energy (Ea ) calculation is a fundamental aspect of understanding the
interaction between adsorbate species and the adsorbent surface. This interaction is
crucial in various fields such as catalysis, surface science, materials science, and
environmental science. [How strongly an adsorbate binds to the surface]

Ea = - (Esystem - (Eadsorbent + Eadsorbate))

Esystem : Total energy of the system when

adsorbate is attached to the adsorbent.
Eadsorbent : Energy of the clean surface.
Eadsorbate : Energy of the isolated adsorbate
molecule.
More negative Ea value corresponds to a
stronger adsorption.
materials square
The Density of States (DOS)

• DOS represents the number of available electronic states per unit energy and volume.
Helpful to obtain electronic structure.
• Info: band gap size, which is the energy difference between the valence band
maximum (VBM) and the conduction band minimum (CBM), and the electrical
properties of various substances, (metals, insulators, or semiconductors).
• DOS and Material Modification: By comparing
the DOS of a pure material with that of a doped
one (for instance, silicon doped with oxygen),
we can infer how the introduction of a new
element alters the electronic states and overall
properties of the material. This is particularly
useful in material design and engineering for
specific applications.
NEB
Nudged Elastic Band (NEB) in Quantum Espresso

Purpose: NEB is a method used to determine the most favorable pathway (or the
minimum energy path) between two given atomic configurations, often representing
initial and final states.

Relevance in DFT: In DFT simulations, NEB helps in studying reaction pathways, identifying
transition states, and estimating energy barriers.

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=smQS4U5Roco&t=310s