DJMOL web documentation

Table of content:

• Table of contents :: DJMOL web documentation

Chapter-1:

• Chapter 1: Introduction
  • Computational Tools
  • Major Components of the Software

Chapter-2:

• Chapter 2: DFTB+ Calculations
  • DFTB+ Script Writer
  • Executing DFTB+ Scripts
  • Force Components
  • Molecular Orbitals and Energy Levels
  • UV-Visible Spectrum Convolution
  • Partial Charges
  • Molecular-Vibrations
  • Real Time Molecular Dynamics
  • Potential Energy Surfaces (2D/1D)

Chapter-3:

• Chapter 3: Modeling with Siesta
  • Siesta Script Writer
  • Siesta Add-On and Executing the Program
  • Basic analayzers
  • Wannier Orbitals and Band Diagrams
  • Molecular Vibrations

Chapter-4:

• Chapter 4: OpenMD Simulations

Chapter-5:

• Chapter 5: Python scripting with ASE

Chapter-6:

• Chapter 6: Tools of DJMol
  • Analysing Point Group
  • Z-Matrix Editor
    • Changing Z-Mat Data
  • Remote Submission of Scripts
  • Version Control using GIT
  • Database File Retrieving
  • Miscellaneous Tools

Chapter-7:

• Chapter 7: Architecture of the Program
  • Software Architecture

Chapter-8:

• Chapter 8: Software Applications
  • Demonstration of DJMol
    • UV-Visible Spectrum of Silver Nanocluster using DFTB+
    • Frontier Orbitals of C ₆₀ Calculated with Siesta
    • OpenMD MD simulation of Gold-nanoparticle
    • ASE simulation of an adatom diffusion

Appendices:

• Appendices
  • Appendix-A
    • Python Scripting for DJMol Applications
      • How to use Python within the DJMol?
      • Basics of python scripting
      • Variable assignment and Operators
      • String, List, Methods etc.
      • List Manipulation Rules
      • List openrations
      • Methods for the Lists
      • Libraries
    • Basics of ASE scripting
  • Appendix-B
    • Installation of Python and NumPy
      • Python Installation
      • Python Modules Installations
      • NumPy Installation
  • Appendix-C
    • Windows Subsystem Linux in DJMol
      • Setting up the WSL
      • Setting up the Netbeans IDE
  • Appendix-D
    • Saved data
  • Appendix-E
    • Demonstration Videos
  • Appendix-F
    • Compiling/Installation of DJMol and its Add-Ons
      • General Information
      • Compiling Main Program, <DJMolplatform>
      • Installing Program, <DJMolplatform>
      • Compiling Add-On Programs
      • Setting Environment Variables for DJMol(Path, CLASSPATH)