About qBaandi
Team and People
Luminescence Lab
Atomistic Modeling Lab (AML)
Stability Lab
Example 1 - Luminescence
Example 2 - AML (ZnS crystal)
Example 3 - AML (structure modeling)
Example 4 - Stability
VLAtoms - Atomic structure modeling
Periodic Boundary Condition (PBC)
Troubleshooing
About qBaandi

The qBaandi is the thematic web platform for quantum dots that provides functionalities to simulate photo-luminescence, electronic and atomic structures, and chemical stability.

KIST's thematic platfroms were built to offer research environment of material simulations, even to the experimentalists and students who never learned simulations. This platform provides computing facilities and all kinds of software for simulations; atomic structure modeling programs, simulation solvers (DFT, MD, MC, effective mass approximation program and many others), solver GUI and data visualization programs. You don’t need any further software and computers but only need the web browser. The qBaandi /qbandi/ is especialy designed for quantum dots. Users can simulate photo-luminescence and swiching properties of real size quantom dots using effective mass approximation, analyze electronic and optical properties with fully quantum mechanical DFT simulations, and test chemical stability with reactive force field (ReaxFF) molecular dyanmics (MD).

Policies
Free to use for registered users. Commercial usage is not allowed.
Please cite qBaandi if you publish or present results from qBaandi.

Registration
Register with your business email, and send your information to contact email. You will get an email from us after we upgrade your authority.


Powered by SimPL!
The qBaandi was developed using SimPL: the Simulation Platform Creator, which is the contents management system of simulation web soft wares and platforms. Visit the SimPL webpage for detail.




Support
The qBaandi project was supported by Nano·Material Technology Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (Grant. NRF-2016M3A7B4024131).
The computing resource is provied by Computational Science Research Center at KIST

The qBaandi Team
PI: Dr Seungchul Kim (KIST)
SimPL and web program and design: Virtual Lab Inc. (Jungho Lee, Semi Jang and Yerang Yu)
Luminescence Lab:
Yong-Hoon Kim’s group at KAIST
Atomistic Modeling Lab: Computational Science Research Center at KIST (Seungchul Kim, Assel Kembay, Sowon Kim)
Stability Lab: Computational Science Research Center at KIST (Sang Soo Han,), Virtual Lab Inc.
Introduction
This lab provides optical properties of nanostructure such as optical gap estimation, PL spectrum, PL switching using first-principles-derived effective mass approximation[2].

How to use?
1. Generate a sample by selecting the simulation geometry.
2. Select materials and nano-parameter(electron effective mass, hole effective mass, dielectric constant)
3. Save the sample.
4. Run calculation.
Electronic structures.
Electronic structures calculated by first-principles-derived effective mass approximation.
It shows the shape of wave function for each eigenvalue from Schrodinger equation.
Photo Luminance.
Photo Luminance shows optical properties of nano-structure.
It shows the PL intensity and optical gap from first-principles-derived effective mass approximation.
Switching
It shows how optical properties(PL intensity) changed by external electric field.
Limitation and errors.
Potential shape
Luminescence lab in the qBaandi uses fermi-dirac potential shape which user choose geometry shape, but in first-principles-derived effective mass approximation uses kohn-sham smoothing potential.
It can cause some errors in calculation We are going to update soon.
Core shell model
If user choose core/shell model, nano-parameter(effective mass, dielectric constant) are mixed in the ratio of core and shell length, but in first-principles-derived effective mass approximation use nano-parameter from core/shell model.
It can cause some errors in calculation We are going to update soon.
Computational detail
Theory : first-principles-derived effective mass approximation
Software : OORI-QNANO
Dependency
System : Python
SimPL Plugin : OORI_PARA
Solver : OORI-QNANO_1
Configuration
It should be using with solver “OORI-QNANO_1” (solver id : 4).
Input parameters
Variable name Type Default Description Remarks
Core Selection CdS Core material in Quantum Dot. Required
Shell Selection None Shell material in Quantum Dot. Required
m*_e / m*_h Real Number NULL Effective mass Required
epsilon Real Number NULL Dielectric constant Required
nstate Integer 3 The number of states in Quantum Dot Required
E-Field Real Number 0.0 Electric field applied on Quantum Dot Remarks
Input parameters
Name Type Description
Eigenvalues Real Number DescriptionAllowed energy levels in Quantum Dot
Wavefunction 3D array Wavefunction of the specific specific states (format : vasp CHGCAR)
Technical information
The key equations of object oriented real-space initiative (OORI) code [1] to perform EMA simulations, are as below. The electron wavefunctions are obtained by solving the Schrödinger equation
References
[1] Y.-H. Kim, I.-H. Lee, and R. M. Martin, Comput. Phys. Commun. 131, 10 (2000).
[2] H. Yeo, J. Lee, and Y.-H. Kim., J. Phys.: Mater. 3, 034012 (2020)


This lab provides functionalities of (1) building atomistic models of quantum dots and nano-structured semiconductors, (2) relaxing the atomic structures to the minimum energy structures, and (3) various electronic structure data such as projected density of states (PDOS), net charge of each atoms, position-dos map, and spin density. SIESTA code [1], which utilizes density functional theory, is used for all calculations.

How to use?
1. Building a sample (the atomic structure of material). Check "VLAtoms - Atomic structure modeling program" before doing simulations.
2. Save the sample.
3. Run Structure Stabilizer. This step takes several hours or days.
4. Load Electronic structure data.

1. Building a sample : Select the structure you want and click the Bulid button.


2. Save the sample : Write the sample name you want and click the Save button


3. Run Structure Stabilizer : Click the button to start relaxation.




Wait until the calculation is finished




4. Load Electronic structure data : Load Electronic structures after calculation.



Building a Sample

There are three ways of building a sample.
1. Use VLAtoms, the atomic structure visualizing and manipulating software, from the page. (See the VLAtoms document to learn how to use it.)
2. Load a sample, modify and save in a different name.
3. Upload user’s own structures. VASP-POSCAR, cif, and xyz formats are supported so far. If your file is not in those format, you may use other programs to convert into cif or POSCAR. VESTA [4] and VLAtoms in MaterialsSquare [5] are recommended.

Be careful on the Periodic Boundary. qBaandi uses periodic boundary condition that atoms in the unit cell are periodically repeated in all three directions. So, even if a few number of atoms in the unit cell, the sample is infinite. If there is vacuum or empty space in your unit cell in any direction, uncheck the Periodic Boundary in that direction. For example, if the sample is for a surface of the solid, having vacuum in ‘z’-direction, uncheck ‘z’ then save. See the document of Periodic Boundary Condition for more information.

Structure Stabilizer

Before calculating electronic structures, qBaandi relaxes atomic structures; it moves atoms a little by little until the forces acting on every atom become negligibly small. This means the atomic structure of the sample reaches to the (local) minimum energy structure. Density functional theory (DFT) calculation is used here, so it takes several hours, for ~ 20 atoms, and days, for ~200 atoms. It is strongly recommend to use less than 200 atoms.

Electronic Structures
Electonic structures calculated using Kohn-Sham DFT, within generalized gradient approxamation (GGA-PBE).
Menu Description
Projected DOS Electronic density of states projected onto atomic orbitals. Muliken population method is used.
Atomic Charge Net charge and spin of each atom. Mulliken population is used.
Position-DOS map It displays electronic density of states along one of x, y, or z direction. It is useful for defective, surface and interface structures, visualizing position of defect, interface or surface states located in the gap, or band offset.
Spin densityVisualization of 3-dimensional spin density (ρspin(r) = nup(r) - ndown(r)). You can download spin density in finer grid. It is written in Gaussian cube format, so that you can draw in various visualization SW, such as VESTA.
Photo Absorption Dielectric functions, absorption coefficient and optical conductivity.
Valence Band Maximum Visualization of 3-dimensional valence band maximum (VBM).
Conduction Band Minimum Visualization of 3-dimensional conduction band minimum (CBM).


Limitation and errors

Band gap : Atomistic Modeling Lab in the qBaandi uses Kohn-Sham DFT within generalized gradient approximation (GGA). This approximation accurately predicts bond energy and geometris, but severely underestimate the size of band gap in general. As the result, band gap, location of in-gap state, and band offset must have large error. This is fundamental problem in GGA. We are going to update to other approximation giving reliable band gap, soon.

Photo Absorption The imaginary part of the dielectric function is calculated using the dipolar transition between Kohn-Sham eigenfunctions, then the real part is obtained using Kramers-Kroning relation. The Drude term is necessary for metal, in general, but it is ignored because qBaandi is made for simulating semiconductors.

Sample size : DFT calculations consume compuational resource very much, and computation time increase ~ Natom3. For example, if 10-atom sample took 10 minutes, 20-atom sample will take 80 minutes. For this reason, users have to make the sample very carefully to minimize computing time.


Computational detail

Theory Kohn-Sham density functional theory (DFT)
Approximation PBE functional in Generalized Gradient Approximation (GGA) class. [2]
Software SIESTA-4.1-b4
Relaxation type Relax unit cell and atomic position for bulk (i.e. periodic in x, y, and z); Relax atomic positions with fixed unit cell for slabs (2D), wires (1D), and molecules (0D)
Pseudo-potential Troullier-Martin type norm-conserving pseudopotential [3]; Scalar relativistic correction; non-linear core correction
Basis function Double-zeta polarization (DZP) of pseudo-atomic orbitals
k-point grid 15 Angstrom of k-grid cutoff. For example, 3 points in 10 Angstrom, 1 point in 30 Angstrom cell
Cutoff energy 300 Ry for electron density (Meshcutoff)
SCF tolerance 0.00005 for density matrix elements (SCF.DM.Tolerance), and 0.002 eV for Hamiltonian matrix elements (SCF.H.Tolerance).
Force tolerance 0.04 eV/Ang (MD.MaxForceTol)
Non-SCF k-point grid Three times denser than scf. If 3x3x3 k-grid is used in scf and structure relaxation calculations, 9x9x9 k-grid is used in PDOS and optical calculations. It is used for DOS calculations (PDOS.kgrid.MonkhorstPack in SIESTA parameters)
Optical mesh Same as k-grid for Non-SCF calculations. It is three times denser than k-point grid in scf calculations in all three directions. (Optical.Mesh in SIESTA parameters)

References
[1] “The SIESTA method for ab initio order-N materials simulation”, José M Soler, Emilio Artacho, Julian D Gale, Alberto García, Javier Junquera, Pablo Ordejón and Daniel Sánchez-Portal, Journal of Physics: Condensed Matter, Volume 14, Number 11; https://departments.icmab.es/leem/siesta ; https://launchpad.net/siesta
[2] Generalized Gradient Approximation Made Simple, John P. Perdew, Kieron Burke, and Matthias Ernzerhof, Phys. Rev. Lett. 77, 3865
[3] “Efficient pseudopotentials for plane-wave calculations”, N. Troullier and José Luís Martins, Phys. Rev. B 43, 1993
[4] VESTA; https://jp-minerals.org/vesta/en
[5] Materials Square provides commercial for DFT calculations, but structure modeling is free. https://www.materialssquare.com
Experimental -- This lab is still under construction.


This lab provides functionalities of checking chemical stability of quantum dots using reactive molecular dynamics.

How to use?
1. Building a sample. Vacuume is necessary to fill up with water or oxygem molecules. Check "VLAtoms - Atomic structure modeling program" before doing simulations.
2. Fill up the vacuum with water or oxygen molecules.
3. Save the sample.
3. Set the temperature and time of simulations.

Limitation and errors

Combination of elements Elemental combinations available in KiFF[3]. Other combination is not able to calculate.

Sample size and time : Reactive molecular dynamics is very heavy, so, the number of atoms were limited by 3000 atoms.


Computational detail

Method Molecular dynamics
Potential Reactive force field [2]
Software LAMMPS
Thermostate NVT
MD time step 1 fs

References
[1]
[2] ReaxFF -- Reactive Force Field
[2] LAMMPS Molecular Dynamics Simulator
[3] http://kiff.vfab.org/reax
Examples for Luminescence lab

1. Core Only

| Core only model calculation :
1) Generate a sample by selecting the simulation geometry.


2) Select materials and nano-parameter
(electron effective mass, hole effective mass, dielectric constant)
3) Save the sample.



4) Run calculation.
| Calculation check
1) Electronic Structure
Electronic structures calculated by first-principles-derived effective mass approximation.
It shows the shape of wave function for each eigenvalue from Schrodinger equation.
2) Photo Luminance
Photo Luminance shows optical properties of nano-structure.
It shows the PL intensity and optical gap from first-principles-derived effective mass approximation.
3) Switching
It shows how optical properties(PL intensity) changed by external electric field.

2. Core / Shell

| Core only model calculation :
1) Generate a sample by selecting the simulation geometry.
In core/shell model calculation, core and shell ratio mush be selected
2) Select materials and nano-parameter(electron effective mass, hole effective mass, dielectric constant)
In core/shell model calculation, core and shell material and nano-parameter must be selected.
3) Save the sample.



4) Run calculation.

3. Manual

| Modeling model calculation :
1) Generate a sample by selecting the simulation geometry.
If you want to calulate the other model, you can choose manual
2) Select materials and nano-parameter(electron effective mass, hole effective mass, dielectric constant)
In manual model calculation, nano-parameter are freely selectable. And you can select bulk optical gap which is used for the calculation.
3) Save the sample.



4) Run calculation.
Examples for atomistic modeling lab

➤ Single crystal structure : Select crystal from the preset ➟ Load a single crystal sturcture.
: The loaded crystal structure is an indefinitely repeated cell (Periodic boundary condition).



Calculation check
: Check if the data to be loaded has been calculated.



When the scf calculation and the relaxation calculation are completed, the calculation is done.
Sometimes the data is zero even if the calculation is completed. (Ex: Spin density)

Projected-DOS (PDOS)
Electronic density of states projected onto atomic orbitals. Muliken population method is used.
x Axis: E-EF / y Axis: Density Of State

➤ You can choose the atoms or orbitals to see.
Select atom


Orbital check box


Atomic Charge
: Net charge and spin of each atom. Mulliken population is used.



When you select an atom using Select Atom, you can see information about the atom.


Position-DOS map
It displays electronic density of states along one of x, y, or z direction.
It is useful for defective, surface and interface structures, visualizing position of defect, interface or surface states located in the gap, or band offset.



Spin Density
Visualization of 3-dimensional spin density (ρspin(r) = nup(r) - ndown(r)).
You can download spin density in finer grid. It is written in Gaussian cube format, so that you can draw in various visualization SW, such as VESTA.



If you want to download, click the Download button (.cube format)

Optical Properties
Dielectric functions, absorption coefficient and optical conductivity.
Click the index of each graph to see only the parts you want.

Dielectric function


Absorption property / Optical conductivity

1. ZnS surface

Surface structure :

(Make a vacuum)

Because we use an indefinitely repeated cell,
It is impossible to create a crystal in which only one side is vacuumed.
➥ We make a structure with vacuum on both sides.


① Modify a structure :

There are various functions that can change the shape of crystal.
Cleave: Cleave surface in miller index/ Clone: Change the unit cell size


② Create a Vacuum Structure
: (Approximately 5Å can make enough vacuum).
③ Surface passivation :
The atoms in contact with the vacuum are often unstable.
➥In that case, surface passivation can be used.(Using pseudoH)

( This function works well for atoms in presets ; an atom with a coordination number of four )

④ Caution before saving ‼ :

The Periodic Boundary in the direction of vacuum must be Unchecked.
(To avoid calculating in the vacuum direction.)





2. C(Diamond)-Si interface(1)

➤ Atom Change : When you want to see more than one substance, Use the Change.
➥ 1.Select the desired atom / 2. Click the Change Button / 3. Enter which one to replace.

( If the lattice constant difference is large, it will take a unrealistic strain. )


➤ TIP : Junction + Surface passivation
: Surface passivation can be used to increase the stability of the Junction.

Remove the PesudoH atoms between substances.


2. C(Diamond)-Si interface(2) : Commensurate cell of two incommensurate lattices
➤Junction. : Gernerate common supercell of two solid surfaces .
➥ it is difficult to fully commensurate the two cells, so set the strain tolerance on the upper structure.

① Clikc the Junction Button
② Upload the structural file of the material structure you have.
③ Click the Gernerate Junction list Button





④ Click the Gererate Junction Button
Choose structure you want from the Junction list. (Enter the index you want.)


➤ TIP: Download the file you want to analyze
➥ You can download structure files by right-clicking during the Building a sample process.



3. Various ways to make Cells

➤ nano-wire from a crystal



➤ Core/Shell structure (CdS-ZnS)



✓ Caution before saving ‼
: The Periodic Boundary in the direction of vacuum must be Unchecked.


✓ Surface passivation
: Surface passivation can be used to increase the stability of the final structure.


✓ Unit Cell
: Set unit cell in minimum units (because it's a cell that repeats indefinitely)

Under construction
What is VLAtoms?
http://simpl.vfab.org/about_vls How to use VLAtoms?
Surface generation
Junciton generation
Build molecules and ligands.
It is incovenient to make molecules using the minimum VLAtoms, which is installed in qBaandi, but it is possible to build.





Everything is repeated infinitely.

Except molecules and sub-nm particles, materials consists of vast amount of atoms, so it is not able to take every individual atom into account to the calculations. To solve this problem in atomistic modelling, people conventionally assumes that a group of atoms repeats periodically to form a large object, similar to single crystal in crystallography, and this is called the periodic boundary condition (PBC). In PBC, there is a unit cell which is defined by three cell vectors and atoms in it, and the unit cell is repeated in all three directions, just like a single crystal. However, even things that are not actually repetitive are repeated in PBC, such as atomic defect in solids or adsorbed chemicals on solid surfaces. The PBC is a mathematical tools that allows computation of large size of materials, comparing to atomic size, with limited computational resources.
Be careful! You have to consider whether your ‘periodic’ model structure is suitable to describe real material.


How large vacuum?

At least 10 Angstrom of vacuum between neighbor unit cell is neccessary, 15-20 Angstrom is recommended.
Suppose you are simulating surface of a solid, and the z-axis is the surface normal direction in your atomistic model, you may want to make half-infinite surface model that infinitely thick material and vacuum are facing with each other. However, such structure is impossible because every thing, including empty space, is periodic. Therefore, there is no choice but to make space between atoms in the neighbor unit cells so that interaction between them to be ignorable.

How to set "Periodic Boundary" at the Atomistic Modeling Lab.
1. Bulk (3-D)
Check all three (x, y and z). It is 3-D structures, and there is no vacuum in any direction.


2. surface and 2-D materials
Un-check the surface normal direction in "Periodic Boundary" It is for surfaces of solids and 2-D materials, such as graphene and MoS2 layer. Although the material is not repeated in surface normal direction, the atomic structure is repeated also in the surface normal direction. To remove interaction between neighbored structure, empty space (vacuum) need to be inserted in the surface normal direction.



3. wire, nanotube (1 D)
1D structure needs vacuum in two directions. If the wire axis is parallel to the z-axis, uncheck x and y, and check z. Insert vacuum in x and y directions.

4. nano-particles, molecules (0 D)
Uncheck all directions (x, y and z) and insert vacuum.
What happens if "Periodic Boundary" is improperly set?

Regardless of checking x, y and z in "Periodic Boundary" in the Atomistic Modeling Lab, the atomic structure is periodic. But, "Periodic Boundary" affects speed and accuracy of the calculations. If 'z' is un-checked, number of k-point in 'z' direction for structure stabilizer, DOS and optical calculation set to be 1. If it is checked for the direction having vacuum, the calculation results are accurate but it may takes longer time than it should be. If it is un-checked for the direction having no vacum, the results may not be accurate.

How to check atomic structure outside the unitcell?
Use the "Ghosts" in VLAtoms. Click the right button in the VLAtoms (atomic structure visulaizer) and check "Ghosts". Atoms in the neighbor unit cells will be shown.



Report your problem via email. (contact: contact.vfab@gmail.com)
To efficently check your problem, we recommend you to use format below;

  User name:
  User email:
  Sample name:
  Lab : (e.g. Luminescence Lab, Atomistic Modeling Lab, Stability Lab)
  Menu : (e.g. Structure Stabilizer, Optical)
  Description:

The calculation is failed in the Atomistic Modeling Lab.
Reason In most cases, this is because the calculation was not able to find solution within the allowed computing time. AML uses SIESTA, one of DFT code. DFT uses two iteration loops; the outer loop is to move atoms until the atomic positions reach the minimum energy structure, and the inner loop is to calculate forces acting on each atom. In some cases, these iterative calculation fails to get converged results (i.e. the solution of equation).

Solution Even if your calculation is not completed, the final structure is different from your starting structure. In this case, you may save the final structure in different name, then start calculation with this new structure. If you fails again, check your atomic structure if it is unphysical (i.e. atoms at too close, too many unsaturated atoms, and so on).
If your starting and final structure are the same, the calculation was not even started, or it fails at the first step. Please report for this case.