Tutorials

The sub-pages under this section contain detailed tutorials. You can find specific tutorial from the index below or locate the corresponding entry in the sidebar navigation.

Table of Contents

• Overview
• Jobs via Command Line: you may skip this unless you are an experienced HPC user seeking familiar command line interface while transitioning to Mat3ra. For advanced platform functionality we recommend using web submission as described in subsequent sections.
  • Overview
  • Create, Run, and Inspect a CLI Job
  • QE GPU Job
• Templating
  • Overview
  • Flags by Elemental Composition
  • Magnetic Moment on Atoms by Specie
• Machine Learning (ML)
  • Overview
  • Python ML
    • Training a Regression Model
    • Predictions with Regression
    • Unsupervised Learning with Clustering
    • Training a Classifier
    • Predicting with a Classifier
  • DeePMD (molecular dynamics)
• Density Functional Theory (DFT)
  • Electronic Properties
    • Overview
    • Effective Screening Medium
    • Electronic band structure
    • Electronic band structure, HSE (QE)
    • Electronic band structure, HSE (VASP)
    • Electronic band structure, GW, Full Freq., (QE)
    • Electronic band structure, GW, Plasmon P., (QE)
    • Electronic band gap
    • Electronic band gap, HSE (QE)
    • Electronic band gap, GW (VASP)
    • Electronic density of states
    • Electronic density mesh
    • Fermi Surface
    • Valence Band Offset
    • Hubbard U (QE)
    • Spin-magnetic (QE)
    • Spin-orbit coupling (QE)
  • Optical Properties
    • Dielectric constant (QE, simple.x)
  • Vibrational Prop.
    • Overview
    • Zero Point Energy
    • Phonons
    • Phonons on Grid
  • Thermodynamic Prop.
    • Surface Energy
  • Chemical Prop.
    • Reaction Energy Profile (QE)
    • Reaction Energy Profile (VASP)
  • Add-ons
    • k-point convergence
    • Structural Relaxation
• General Functionality
  • Accessing the Platform
  • Jupyter Notebook
  • Restart from Previous Job
  • TensorFlow (GPU)

• Materials

  • Overview
  • VESTA via Remote Desktop
  • Combinatorial Sets
  • Interpolated Sets
  • Molecule on a Surface
  • Interface, quick setup (3D Editor)
  • Interface, minimal strain (JupyterLite Session)
  • Import materials from files in various formats

• Reproducing Specific Manuscripts:

  • Substitutional Point Defects in Graphene
  • Vacancy-Substitution Pair Defects in GaN
  • Vacancy Point Defect in h-BN
  • Interstitial Point Defect in SnO
  • Island Surface Defect Formation in TiN
  • Step Surface Defect on Pt(111)
  • Twisted Bilayer h-BN nanoribbons
  • Twisted Bilayer MoS2 commensurate lattices
  • Adatom Surface Defects on Graphene
  • H-Passivated Silicon Nanowire
  • H-Passivated Silicon (100) Surface
  • Gold Nanoclusters
  • SrTiO3 Slab
  • Interface between Graphene and h-BN
  • Interface between Copper and SiO2 (Cristobalite)
  • Interface between Graphene and SiO2 (alpha-quartz)
  • High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)
  • Ripple perturbation of a Graphene sheet
  • Grain Boundary in FCC Metals (Copper)
  • Grain Boundary (2D) in h-BN
  • Gr/Ni(111) Interface Optimization
  • Pt Adatoms Island on MoS2