Pre-processing
VQkit pre-processing provides calculation setup, structure editing, validation, pseudopotential management, reciprocal-space/convergence tools, and NEB image preparation for VASP and Quantum ESPRESSO.
- Calculation Setup
- Structure Editing
- Height and layer analysis
- Layer detection
- Supported input structures
- [4] Freeze / fix atoms
- Choose fixed direction
- How VQkit represents constraints
- Selecting atoms to fix
- Selection by height
- Selection by layers
- Selection by atom index
- Output file for freeze/fix workflow
- Existing output protection
- QE atom ordering and mapping
- Example: freeze bottom two VASP layers
- Example: fix only z motion in QE
- [5] Delete atoms
- Selecting atoms to delete
- Selection by atom label/type
- Selection by layers
- Selection by height
- Deletion summary
- Delete-atoms output files
- VASP deletion behavior
- Quantum ESPRESSO deletion behavior
- Example: remove an adsorbate
- Example: remove the top slab layer
- Important scientific checks after editing
- Height-based selection cautions
- Layer tolerance
- Recommended workflow
- Validation
- Meaning of report levels
- Code detection
- VASP pre-flight validation
- INCAR checks
- Repeated INCAR tags
- Spin setup
- Ionic-relaxation consistency
- POSCAR checks
- POTCAR checks
- ENCUT versus ENMAX
- KPOINTS validation
- HPC job script
- VASP example report
- Quantum ESPRESSO pre-flight validation
- Required QE namelists
- nat and ntyp
- ATOMIC_SPECIES
- ATOMIC_POSITIONS
- Lattice validation
- Plane-wave cutoffs
- K_POINTS validation
- Relaxation-specific checks
- Smearing consistency
- Calculation identity
- pseudo_dir validation
- Pseudopotential file validation
- outdir
- QE example report
- READY logic
- What the checker does not validate
- Recommended workflow
- Scientific responsibility
- Pseudopotentials
- Why pseudopotential configuration matters
- [8] Pseudopotential library setup
- 1. Configure VASP POTCAR library
- 2. Configure Quantum ESPRESSO UPF library
- 3. Show configured pseudopotential libraries
- 4. VQkit private pseudopotential folders
- VASP licensing note
- [7] Create POTCAR from POSCAR
- POTCAR assembly
- Missing potential
- Existing POTCAR
- Automatic POTCAR creation during calculation setup
- Example: VASP Fe-O calculation
- POTCAR and ENCUT
- Example: Quantum ESPRESSO library setup
- Scientific selection of pseudopotentials
- Common problems
- Licensing and redistribution
- Recommended workflow
- Reciprocal Space and Convergence
- [9] Generate band-structure K-path
- Symmetry tolerance scan
- Symmetry-standardized path
- Interpolation density
- VASP path output
- Quantum ESPRESSO path output
- Built-in fallback path library
- Band-path cautions
- [10] K-points
- Supported structures
- Reciprocal lattice
- Automatic k-spacing
- Mesh formula
- System dimensionality
- Vacuum-gap estimation
- Automatic dimensionality
- 2D systems
- 1D systems
- 3D systems
- Monkhorst-Pack mesh
- Gamma-centered mesh
- QE Monkhorst-Pack shifts
- Irreducible k-points
- Manual k-point mesh
- K-point scientific cautions
- [11] Convergence tests
- VASP cutoff preparation
- Quantum ESPRESSO cutoff preparation
- Execution modes
- Analyze completed cutoff calculations
- Energy extraction
- Reference energy
- Recommended cutoff logic
- Generated convergence outputs
- Example: VASP cutoff convergence
- Example: QE cutoff convergence
- Convergence-test cautions
- Recommended workflow
- NEB Pre-processing
- NEB concept
- Open the NEB image generator
- VASP NEB preparation
- VASP endpoint requirements
- VASP interpolation cautions
- Recommended VASP workflow
- Quantum ESPRESSO NEB preparation
- QE NEB output file
- QE CIF inspection images
- Visual validation
- What to inspect in every image
- QE execution
- Review before running QE NEB
- Climbing-image NEB
- Number of images
- Cell consistency
- Periodic boundary conditions
- Atom ordering
- Endpoint optimization
- VASP preparation after interpolation
- Quantum ESPRESSO preparation after interpolation
- NEB convergence
- Transition-state interpretation
- Recommended VASP example
- Recommended QE example
- Connection to NEB post-processing
- Scientific cautions
- Recommended workflow