Post-processing

VQkit post-processing analyzes completed VASP and Quantum ESPRESSO calculations through a common file-based interface.

• General Calculation Analysis
  • Example
  • Basic workflow
  • Information reported
  • Code detection
  • Calculation-type detection
  • VASP status detection
  • Quantum ESPRESSO status detection
  • Input/output association
  • VASP total-energy extraction
  • Quantum ESPRESSO total-energy extraction
  • VASP Fermi-level extraction
  • Quantum ESPRESSO Fermi-level extraction
  • Example: completed VASP SCF
  • Example: completed QE SCF
  • Example: incomplete calculation
  • Interpreting the status correctly
  • Mixed directories
  • Why the summary is useful
  • Recommended post-processing sequence
  • Scientific cautions
  • Summary limitations
  • Recommended practice
• Structural Analysis
  • Overview
  • VASP example
  • Quantum ESPRESSO example
  • Final-structure detection
  • Optimized structure / lattice / volume
  • Converting the final structure to a new input
  • Bond-length analysis
  • Choosing a bond cutoff
  • Bond-angle analysis
  • Atomic-height analysis
  • Layer analysis
  • Using layer analysis for slab systems
  • Choosing the layer tolerance
  • Example: analyze a relaxed VASP slab
  • Example: analyze a relaxed QE structure
  • Minimum-image convention
  • Scientific cautions
  • Recommended workflow
  • Generated files
• Electronic Structure
  • General workflow
  • DOS - VASP
  • DOS - Quantum ESPRESSO
  • Projected DOS (PDOS)
  • Band structure - VASP
  • Band structure - Quantum ESPRESSO
  • Band outputs
  • Spin-polarized bands
  • Band-gap analysis
  • Band-gap cautions
  • Fermi energy
  • Work function
  • Quantum ESPRESSO work function
  • Work-function outputs
  • Relationship between the six menu items
  • Recommended analysis sequence
  • Common cautions
  • Generated files summary
• Charge Density, Bader Charge, and ELF
  • Charge-density difference
  • CDD cube parsing
  • CDD plotting menu
  • CDD color convention
  • CDD outputs
  • Three-dimensional visualization
  • CDD interpretation cautions
  • Bader charge analysis
  • External dependency
  • Bader file-status check
  • Reference-density preparation
  • Running Bader analysis
  • Analyzing an existing ACF.dat
  • POTCAR ZVAL and net charge
  • Bader output
  • Additional ACF information
  • Bader interpretation cautions
  • Electron localization function
  • ELF range
  • ELF plotting menu
  • ELF contours
  • QE ELF preparation
  • ELF outputs
  • Three-dimensional ELF
  • Relationship between CDD, Bader, and ELF
  • Recommended combined workflow
  • Tutorial links
• Energetics and Thermodynamics
  • Detected calculation and status
  • [1] Atom / molecule adsorption energy
  • [2] Doping formation energy
  • [3] NEB / transition-state analysis and plot
  • [4] Surface energy
  • [5] Single-atom vacancy formation energy
  • Common requirements for energetic comparisons
  • Energy versus free energy
  • Recommended workflow
  • Generated files summary
• AIMD / Trajectory Analysis
  • General AIMD requirements
  • Time-step detection
  • Time convention
  • Variable-cell / NPT trajectories
  • Common XDATCAR prompt
  • Coordinate handling
  • Periodic unwrapping
  • [1] Trajectory summary
  • [2] Atomic position coordinates vs time
  • [3] Energy vs time
  • [4] Volume / lattice parameters vs time
  • [5] Bond distance vs time
  • [6] Mean-square displacement (MSD)
  • [7] Diffusion coefficient
  • [8] Radial distribution function (RDF)
  • [9] Coordination number vs time
  • Atom and group selection
  • Example: Li-ion diffusion
  • Example: bond-breaking trajectory
  • Example: liquid structure
  • Output directory summary
  • Plot generation
  • Important scientific cautions
  • Recommended AIMD analysis sequence
• Batteries
  • Cathode material analysis
  • Anode material analysis
  • Chemical-formula mass parser
  • Reference consistency
  • Li metal reference
  • Formula-unit normalization
  • 0 K approximation
  • Cathode stability versus full phase stability
  • Diffusion caution
  • Recommended cathode workflow
  • Recommended anode workflow
  • Connection to other VQkit modules
  • Current scope
  • Summary
• Catalysis
  • Computational hydrogen electrode
  • [1] ORR free-energy analysis (CHE)
  • [2] OER free-energy analysis (CHE)
  • ORR/OER free-energy diagrams
  • [3] HER analysis
  • [4] CO2RR analysis
  • [5] NRR analysis (CHE)
  • [6] CO reduction (CORR) analysis
  • [7] Vibrational frequency analysis
  • [8] Orbital center (s/p/d)
  • Catalysis workflow relationships
  • Recommended ORR/OER workflow
  • Recommended HER workflow
  • Recommended CO2RR workflow
  • Recommended NRR/CORR workflow
  • Thermochemistry consistency
  • Scientific limitations
  • Summary
• Mechanical / Structural Properties
  • Elastic tensor
  • Voigt strain convention
  • Default strain grid
  • [1] Prepare elastic calculations
  • Source structures
  • Metric lattice-family detection
  • General elastic mode
  • Symmetry-reduced mode
  • Energy-strain method
  • VASP preparation
  • Quantum ESPRESSO preparation
  • Output directories
  • Manifest file
  • Stress-strain method
  • Stress-strain accuracy
  • [2] Analyze completed elastic calculations
  • Energy-strain fitting
  • Stress-strain fitting
  • Raw stress stiffness tensor
  • Elastic stiffness tensor
  • Compliance tensor
  • Voigt-Reuss-Hill properties
  • Elastic anisotropy
  • Mechanical stability
  • Mechanical output summary
  • [3] Directional elasticity: high-accuracy 3D plots
  • Positive-definite requirement
  • Young’s modulus
  • Linear compressibility
  • Shear modulus
  • Poisson ratio
  • High-resolution grid
  • ELATE-compatible optimization
  • Automatic directional extrema
  • Directional output directory
  • Directional summary
  • Recommended elastic workflow
  • Energy-strain versus stress-strain
  • Scientific cautions
  • Summary
• Phonon-Derived Transport Properties
  • [1] Phonon group velocity
  • Supported dispersion-table formats
  • Source-unit selection
  • Group-velocity conversion
  • Segment-aware differentiation
  • Branch-resolved velocities
  • Acoustic-mode estimate near Gamma
  • Acoustic RMS velocity
  • Group-velocity cautions
  • [2] Gruneisen parameter
  • [1] gruneisen_band.dat
  • Acoustic RMS Gruneisen parameter
  • Two-volume Gruneisen calculation
  • Non-positive frequencies
  • Folder-based workflow
  • Volume-span warning
  • Gruneisen outputs
  • Scientific interpretation
  • [3] Debye temperature
  • Automatic Debye workflow
  • Velocity-based Debye temperature
  • Automatic Debye output
  • Maximum-frequency estimate
  • Manual acoustic-velocity mode
  • Relationship among the three descriptors
  • Recommended workflow
  • Scientific cautions
  • Generated files summary
  • Summary
• Supercapacitor
  • [1] Quantum capacitance from DOS
  • DOS source
  • Spin-polarized DOS
  • Fermi-Dirac derivative
  • Effective DOS
  • Area conversion
  • Electrode-area input
  • Temperature
  • Potential modes
  • Potential-dependent output
  • Quantum-capacitance summary
  • Plots
  • Low-temperature limit
  • Example quantum-capacitance workflow
  • [2] Total interfacial capacitance
  • Input
  • Physical interpretation
  • [3] Show equations / conventions
  • Quantum capacitance versus double-layer capacitance
  • DOS convergence
  • Energy window
  • Electrode area
  • One-sided versus two-sided electrodes
  • Potential convention
  • Temperature dependence
  • Supercapacitor limitations
  • Pseudocapacitive materials
  • Recommended workflow
  • Connection to other VQkit modules
  • Generated files summary
  • Summary