Tutorials

Table of Contents

• Geometry of a water molecule
  • Introduction
  • Prerequisites
  • Preliminaries
  • Building the molecule
  • Visualizing the molecule
  • Querying the molecule
  • Finding an energetic minimum
  • Calculating the energetic minimum
  • Relaxing the molecule
  • Summing up
• Calculating molecular properties
  • Introduction
  • Prerequisites
  • Getting started
  • Solving the electronic structure problem
    • Increasing verbosity
  • Investigating parameter effects
    • Optimizing the real-space grid density
    • Selecting a suitable basis set
    • The exchange correlation functional
  • The Kohn-Sham eigenvalue spectrum
  • Visualizing Kohn-Sham eigenstates
  • Mulliken populations
• Spin-polarized oxygen
  • Introduction
  • Prerequisites
  • Creating the molecule
  • Total energy and equilibrium distance
  • Adding spin-polarized electron density
  • Three different states
  • Optimized bond distance
  • Summary
• The band structure of bulk silicon
  • Introduction
  • Prerequisites
  • Introduction to periodic systems
    • Creating and examining a periodic configuration
    • k-point sampling
  • The band structure of bulk Si
    • The self-consistent calculation
    • Calculating and visualizing Bloch states
    • Setting up symmetry points and lines
    • Calculating the band structure
    • Exporting the band structure
• Spin-polarized iron
  • Introduction
  • Prerequisites
  • Creating the sample
  • Defining and executing the calculation
  • Plotting the band structure
    • Plotting using matplotlib
  • The complete script
  • Summary
  • Imported modules
    • bandstructure.py
    • separations.py
• Li-H₂-Li two-probe system
  • Introduction
  • Prerequisites
    • Basic concepts of a two-probe setup
  • Constructing the two-probe system
    • Constructing the lithium electrodes
    • Constructing the central scattering region
    • Combining electrodes and scattering region
    • Exporting the structure to a VNLFile
    • The input file
  • Performing a self-consistent calculation for the two-probe system
    • Importing the structure from a VNL file
    • Configuring the calculation
    • The input file
    • Running the calculation
  • Analyzing the two-probe system
    • Loading a previous calculation
    • Calculating the transmission spectrum
    • Conductance
  • The current as a function of bias
    • The input file
    • Current-voltage curve
  • Advanced geometry setup
  • Summing up
• Transmission eigenchannels of doped Al wire
  • Introduction
  • Prerequisites
  • Two-probe perfect Al wire
    • Electrodes
    • Central scattering region
    • Assembling the Two-probe system
    • The input file
    • Configuring and Performing a SCF calculation
    • Transmission spectrum
    • Transmission eigenchannels
  • Two-probe doped Al wire
    • Assembling the Two-probe system
    • Performing a SCF
    • Transmission spectrum
    • Transmission eigenchannels
  • Summing up
• Optimizing a lithium chain
  • Introduction
  • Prerequisites
  • Setting up the pieces
    • Choosing the basis
  • Calculating the total energy
  • Finding the lattice constant
• Optimizing a two-probe system
  • Introduction
  • Prerequisites
  • Setting up the initial configuration
  • Performing the optimization
  • Comparing the transmission eigenstates
• Further analysis of two-probe systems
  • Introduction
  • Prerequisites
  • Projected eigenstates
    • Calculating the projected energy spectrum
    • Visualizing the eigenstates of the projected spectrum
  • Voltage drop
  • Local density of states
• Spin-polarized two-probe system
  • Introduction
  • Prerequisites
  • Specifying the two-probe geometry
    • Electrodes
    • Specifying the scattering region layers
    • The complete geometry setup script
  • Configuring and performing the calculation
    • Importing the geometry
    • Defining the spin-polarization
  • Running the self-consistent calculation
    • Serial execution
    • Parallel execution
    • Output files
  • Calculating the conductance and the TMR
  • Summary
• Understanding two-probe geometry
  • Introduction
  • Prerequisites
  • Two-probe preliminaries
  • Understanding the Au (111) crystal structure
  • Stacking the gold layers
  • Setting up the DTB molecule
  • Defining the scattering region
  • Constructing the electrodes
  • Piecing everything together
• Reaction path optimization using the Nudged Elastic Band method
  • Introduction
  • Nudged elastic band
    • Introduction to the Nudged Elastic Band method
    • Example: Dehydrogenation of C₂H₆
    • Example: Restart dehydrogenation of ethane reaction
  • Reference documentation
    • KohnShamSimulation class
    • MDMin class
    • NEB class