THE JISUAN LEARNING NOTEBOOK
Start with quantum chemistry.
Explore materials through computation.
Understand electrons and atoms, then learn to prepare inputs, run calculations, and evaluate results. Connect the equations, VASP parameters, and research questions in a step-by-step learning path.
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Ĥψ = Eψ → ρ(r) → E, F, σ
# Verify numerical accuracy with convergence tests
A PLACE TO BEGIN
Learn through questions.
Support conclusions with evidence.
This manual starts with the core concepts of quantum mechanics and DFT, uses silicon crystals to establish an introductory workflow, and then gradually moves into electronic structure, surface catalysis, and finite temperature tasks. Each parameter example should be read together with its structure, pseudopotential, precomputation, and checking methods.
Define the question
What kind of questions are answered by wavefunction, electron density, energy and force respectively.
Choose the setup
Start with human-readable input and keep units, element order, and methods consistent between files.
Validate the result
Electronic convergence, numerical convergence and physical conclusions are three things that need to be verified separately.
FOLLOW THE LEARNING PATH
Build your understanding, step by step.
Read in order, or enter from specific tasks. The chapters include parameter explanations, input examples, checking steps and common misunderstandings.
Quantum Chemistry & DFT
From wavefunction, energy and electron density, build a physical picture of first-principles calculations.
Your First VASP Calculation
Use a set of silicon primitive cell calculation examples to learn input files, convergence testing, structural optimization and output checking.
Electronic Structure & Properties
Starting from convergent charges, understand band structure, density of states, magnetism, DFT+U and spin–orbit coupling.
Advanced Research Tasks
Extend basic workflows to surfaces, defects, phonons, reaction pathways and finite temperature dynamics.
Parameter Reference & Good Practice
Check parameters by function, check prerequisites by task, and conduct a self-examination before starting to calculate and report results.
Exercises & Self-checks
Organize principles and parameters into calculation plans, data tables, and research records that can be reviewed by others.
FIND YOUR NEXT STEP
What would you like to explore first?
An input file is just the starting point. Select the current target and find the principles and operations you need to understand first.
SEARCH THE NOTEBOOK
Find a concept in context.
Search chapter text that includes all modules; enter multiple words to narrow the scope further.
FILES FOR YOUR FIRST EXPERIMENTS
Bring the examples into your workflow.
The download contains input templates and usage instructions and does not contain the VASP program, POTCAR, WAVECAR or any real calculation results.
First read README.md in the root directory of the compressed package. Files with .template need to replace placeholders, completion structures and prefix files and cannot be submitted directly.
Browse and download individual files (46 files)
Teaching input; need to bring your own authorized Si POTCAR and check ENMAX and convergence.
Silicon SCF · KPOINTS ↓ si-scf/KPOINTSTeaching input; need to bring your own authorized Si POTCAR and check ENMAX and convergence.
Silicone SCF · INCAR ↓ si-scf/INCARTeaching input; need to bring your own authorized Si POTCAR and check ENMAX and convergence.
Silicon SCF · README.txt ↓ si-scf/README.txtTeaching input; need to bring your own authorized Si POTCAR and check ENMAX and convergence.
Silicon unit cell optimization · INCAR ↓ si-relax/INCARPaired with same silicon POSCAR/POTCAR with converged mesh; 520 eV volumetric optimization accuracy must be verified.
Silicon unit cell optimization · Operation instructions ↓ si-relax/README.txtOptimization is not a completed calculation; please verify final forces and stresses.
Silicon Ultimate Static · INCAR ↓ si-static/INCARCopying POSCAR from si-relax/CONTCAR where convergence has been verified, the potential file remains consistent.
Silicon Final Static · KPOINTS ↓ si-static/KPOINTSCopying POSCAR from si-relax/CONTCAR where convergence has been verified, the potential file remains consistent.
Silicon Final Static · Operating Instructions ↓ si-static/README.txtThe downloaded package does not create an optimized structure, you need to complete your own optimization first.
Standalone Convergence Catalog Generator ↓ prepare_convergence.pyOnly generate the directory and input, do not submit or run VASP; will refuse to overwrite the target directory.
Slurm submission template ↓ submit.slurm.templateQueue and module placeholders must be replaced and the launcher adjusted as per Compute Center instructions.
Reproducible calculation records ↓ calculation-record.md.templateFill in after each actual calculation, do not use hypothetical results.
Silicon DOS · INCAR ↓ si-dos/INCARThe converged POSCAR, POTCAR and CHGCAR of the same silicon primitive cell are required; the values are the starting point for teaching to be tested.
Silicon DOS · KPOINTS ↓ si-dos/KPOINTSThe converged POSCAR, POTCAR and CHGCAR of the same silicon primitive cell are required; the values are the starting point for teaching to be tested.
Silicon PBE band structure · INCAR ↓ si-bands/INCARThe converged POSCAR, POTCAR and CHGCAR of the same silicon primitive cell are required; the values are the starting point for teaching to be tested.
Silicon PBE band structure · Path ↓ si-bands/KPOINTSThe converged POSCAR, POTCAR and CHGCAR of the same silicon primitive cell are required; the values are the starting point for teaching to be tested.
Silicon DOS · Preliminary instructions ↓ si-dos/README.txtAvoid confusing ICHARG=1 for a fixed charge density.
Silicon band structure · Preliminary description ↓ si-bands/README.txtThe path only corresponds to the primitive cell of this tutorial and cannot be directly transplanted to other unit cells.
Ferromagnetic initial state exercise · POSCAR ↓ fe-fm/POSCARPrepare your own authorized Fe PAW-PBE potential and redo the Fe convergence test. 2.87 Å is the fixed teaching geometry.
Ferromagnetic initial state exercises · KPOINTS ↓ fe-fm/KPOINTSPrepare your own authorized Fe PAW-PBE potential and redo the Fe convergence test. 2.87 Å is the fixed teaching geometry.
Ferromagnetic initial state exercises · INCAR ↓ fe-fm/INCARPrepare your own authorized Fe PAW-PBE potential and redo the Fe convergence test. 2.87 Å is the fixed teaching geometry.
Initial state of reverse magnetic moment · INCAR ↓ fe-afm/INCARCopies the same structure, mesh and potential of fe-fm; initializes from scratch, does not read existing magnetization density.
Magnetic contrast · Preliminary instructions ↓ fe-afm/README.txtComparing the results requires actual solution, and the reverse initial state may not be maintained until the end.
DFT+U · Template to be configured ↓ dft-u/INCAR.templateExplicitly Not Ready: Requires Ni2O2 magnetic structure, compatible mesh, Ni O potential files, and well-documented Ueff and cutoff energies.
DFT+U · Configure boundaries ↓ dft-u/README.txtAvoid assumptions about the magnetic unit cell or "universal U".
Silicon SOC · INCAR ↓ si-soc/INCARMust use vasp_ncl; package for replicating non-magnetic silicon static structures, potentials, CHGCAR and uniform meshes.
Silicon SOC · Preliminary instructions ↓ si-soc/README.txtThe three-component magnetic moment and the program type must be correct at the same time.
Silicon Charge Analysis · INCAR ↓ si-charge/INCARComes with the same verified structure, potential and convergence mesh; the fine FFT mesh also needs to be verified after LAECHG export.
Charge analysis · Preliminary instructions ↓ si-charge/README.txtDo not treat Bader partition charges directly as integer oxidation states.
Neutral surface optimization template ↓ surface/INCAR.templateRequires slab structure, permission POTCAR, converged k-grid, ENCUT, and DIPOL; examples do not include magnetic or charge states.
Bulk charged defect optimization template ↓ defect/INCAR.templateNeed to supplement the real supercell, k-point, pseudopotential, electron number and spin scheme; does not include automatic formation energy or universal charge correction.
VASP built-in finite displacement template ↓ phonon-internal/INCAR.templateInput unit cell Γ point mode for optimized structures only; requires force accuracy and displacement convergence, not full phonon dispersion.
Phonopy Displacement Structure Static Force Template ↓ phonopy/INCAR-force.templateUsed for each external displacement supercell, prohibiting ion optimization; need to unify parameters, complete structure and pseudopotential.
Phonopy step-by-step command instructions ↓ phonopy/workflow.txt.templateWritten according to the official Phonopy 4.5 command system; the actual displacement quantities and paths need to be replaced, and no real calculations are provided or performed.
Three-dimensional bulk elastic response template ↓ elastic/INCAR.templateIt is only applicable to the fully optimized three-dimensional bulk phase; it needs to converge the stress accuracy and cannot be directly used for the two-dimensional modulus containing vacuum.
Native VASP NEB template ↓ neb-native/INCAR.templateFixed unit cell, five intermediate structures; seven sets of endpoint/intermediate POSCAR required. The native optimizer uses finite POTIM.
CI-NEB optimizer snippet for VTST only ↓ neb-vtst/optimizer-overlay.INCAR.templateNon-complete INCAR; only replaces the corresponding lines of the verified VTST program. Normal VASP prohibits the use of POTIM=0 fragments.
Langevin NVT Molecular Dynamics Template ↓ aimd-nvt/INCAR.templateShort trial calculation of two atom types; the element friction array, time step and production sampling length need to be modified, and no real trajectory is provided.
PBE-D3(BJ) method snippet ↓ vdw/pbe-d3bj-overlay.INCAR.templateSupplementary fragment only, required to be merged into complete and validated PBE input; cannot be blindly stacked with other dispersion schemes.
HSE06 self-consistent static template ↓ hse06/INCAR.templateStatic calculation of nonmagnetic semiconductors from scratch; requires regular k-grid and converged ENCUT, fixed PBE charge density shortcut cannot be used.
PBE independent particle optical template ↓ optics/INCAR.templateSelf-consistent frequency response of a 3D non-magnetic insulator; NBANDS, ENCUT and k-grid all need to converge, excitons excluded.
Semi-local DFT static dielectric template ↓ dielectric/INCAR.templateElectron clamped ion dielectric response with Born charge; does not contain full ion contributions and is not suitable for LEPSILON calculations of HSE.
Advanced template usage instructions ↓ advanced-README.mdRead this first; clarify the limitations that apply to native NEB/VTST, Phonopy versions, and all templates.
Calculation recurrence record template ↓ report/calculation-report.mdBlank research record, including model, method, convergence, operating environment and evidence boundaries; can be filled in according to specific tasks.
Comprehensive practice records and self-examination checklist ↓ report/practice-checklist.mdFillable reporting framework; all results are left blank and do not include simulated data or automated scoring.
OUTCAR summary extraction script ↓ tools/inspect_vasp_run.pyRead-only extraction of last energy and force, stop message, and file hash; no automatic certification of convergence. The Python standard library can be run.
This is a teaching manual based on official materials. The input examples have not yet been verified by VASP calculations case by case. Conditions applicable to the Silicon Getting Started Example, Other Materials Templates, and Analytical Model Demonstrations are stated separately; "End of Calculation" is not a substitute for convergence checks. For software and pseudopotential, please use the version licensed by your research group.