Angze Li Personal computational architecture

Structure → evidence → publication

Computational
modelling workflow

From molecular structure and crystal models to reproducible quantum-chemical and materials modelling.

Finite Periodic Automated Reproducible

Stage-aligned computational architecture

Two systems. Shared structure logic.

Finite and periodic models begin from different structural evidence, meet in a common modelling abstraction, and proceed through aligned validation, calculation, interpretation, and reporting stages.

01 / Finite

Finite / molecular systems

Molecules · dimers · clusters · finite fragments

02 / Periodic

Periodic / extended systems

Crystals · COFs · MOFs · surfaces · defects · interfaces

Input + preparation / Finite

2D chemical identity

ChemDraw

Define molecular connectivity and chemical identity.

  • Connectivity
  • Bond order
  • Protonation
  • Chemical identity

Input + preparation / Periodic

Experimental structural evidence

CIF / structure source

Begin from a traceable crystallographic or measured structure.

  • Literature
  • Crystallographic databases
  • Experimentally measured structures

Initial 3D model

Avogadro 2

Generate and inspect a chemically sensible starting geometry.

  • 3D structure
  • Stereochemistry
  • Proton placement
  • Obvious strain
  • Cheap pre-optimisation

Visual crystal inspection

VESTA

Inspect the cell, coordination, periodicity, and structural plausibility.

  • Crystal sanity checks
  • Cell inspection
  • Coordination environment
  • Later volumetric views

Canonical structural parent

Reference 3D structure

Establish one common monomer or building-block geometry from which downstream finite motifs are generated.

Traceable periodic parent

Reference crystal model

Preserve source, cell choice, and structural provenance before standardisation or supercell construction.

Structure modelling / Shared abstraction

ASE

Reproducible generation and transformation of atomic structures.

Finite / molecular

  • Motifs
  • Dimers / clusters
  • Stacking
  • H-bond arrangements
  • Translation + rotation
  • Slip
  • Distance scans
  • Adsorption geometries

Periodic / extended

  • Supercells
  • Slabs
  • Miller surfaces
  • Vacuum
  • Adsorption
  • Defects + vacancies
  • Dopants
  • Interfaces

Finite / Structure validation

Structure validation

Verify model identity and geometry before electronic-structure work.

  • Composition
  • Atom count
  • Connectivity
  • Minimum distances
  • Expected H-bond distances
  • Reference-geometry consistency
  • Motif metadata
  • Duplicate detection

Periodic / Structure validation

Structure validation

Verify cell, periodicity, and model construction before VASP work.

  • Stoichiometry + cell
  • PBC + dimensionality
  • Symmetry
  • Minimum distances
  • Surface termination
  • Slab thickness
  • Vacuum thickness
  • Duplicate structures

Finite-system quantum chemistry

ORCA

Electronic-structure calculations for molecules and finite clusters.

Geometry + pathways

  • Optimisation
  • Frequencies
  • Transition states
  • IRC / reaction paths

Energetics

  • Single points
  • Interaction energies
  • Redox energetics
  • Thermochemistry / ΔG

Electronic + excited states

  • Orbitals
  • TD-DFT
  • Charge / spin
  • Excited-state properties

Method strategy

Screen / build
r²SCAN-3c Motif scans · pre-optimisation · geometry screening
Production DFT
ωB97X-D4 / ma-def2-TZVP RIJCOSX acceleration Refined energetics · electronic structure
Selected benchmarks
DLPNO-CCSD(T) High-accuracy single points where justified

Environment

  • CPCM
  • SMD
  • Implicit solvation

Wavefunction + properties

  • GBW
  • Molden / wavefunction outputs
  • Spectroscopic properties
  • Downstream analysis

Periodic electronic structure

VASP

Periodic DFT for bulk materials, surfaces, defects, and interfaces.

Pre-production / numerical validation

  • ENCUT
  • k-point density
  • Smearing
  • EDIFF / force criteria
  • Supercell-size convergence where relevant
  • Slab / vacuum convergence where relevant

Reference periodic structure

  • Structural relaxation
  • Lattice optimisation where appropriate
  • Canonical relaxed periodic structure for downstream models

Production branches

Bulk
  • EOS
  • Lattice
  • Stability
Electronic
  • Bands
  • DOS / PDOS
  • Band edges
  • Charge density
Surfaces
  • Slabs
  • Work function
  • Adsorption
  • Intermediates
Defects
  • Vacancies
  • Dopants
  • Defect energetics
  • Localisation
Interfaces
  • Heterojunctions
  • Strain / matching
  • Charge redistribution

Finite / Post-processing

Finite post-processing

Verify ORCA products before deriving wavefunction-based evidence.

01 / Parse + QA

ORCA parsers

Termination · SCF convergence · energies · metadata · provenance

02 / Derive + interpret

Multiwfn

IGMH · ESP · orbital · charge · spin · wavefunction descriptors

Periodic / Post-processing

Periodic post-processing

Verify VASP products before interpreting electronic and charge data.

01 / Parse + QA

pymatgen · VASPKIT

VASP parsing · numerical convergence extraction · structural data · band / DOS · metadata

02 / Interpret + visualise

sumo · Bader · VESTA

Plots · charge partitioning · charge-density / volumetric data · structural visualisation

Scientific validation / Finite

Validated finite result

Calculation products ready for common analysis and comparison.

  • Normal termination
  • SCF convergence
  • Imaginary-frequency checks where relevant
  • Comparable reference states
  • Energy consistency
  • Methodological consistency

Scientific validation / Periodic

Validated periodic result

Calculation products ready for common analysis and comparison.

  • Numerical convergence
  • Comparable cells / reference states
  • Finite-size effects
  • Slab / vacuum adequacy
  • k-point consistency
  • Electronic-structure consistency
  • Comparable defect / surface models

Common analysis layer

Python

Reproducible analysis, comparison, and scientific reporting.

  • NumPy
  • pandas
  • matplotlib
  • Parsing
  • Aggregation
  • Automated QA
  • Statistics
  • Cross-calculation comparison
  • Plotting
  • Report generation

Communicate + preserve / Research products

Scientific output

Publication figures · tables · supporting information · manuscript results

Reports · databases · reusable computational workflows