Tutorials¶

Step-by-step guides for common workflows in NH3-SOFC research.

Getting Started¶

Tutorial	Description	Time
Surface Building	Create surfaces and oxynitride defects	15 min
Adsorbate Placement	6 methods for placing molecules	20 min
VASP Calculations	Generate inputs, parse outputs	25 min

NH3 Decomposition¶

Tutorial	Description	Time
Decomposition Pathway	Complete NH3→N2+H2 workflow	30 min
NEB Transition States	Find reaction barriers	25 min
Frequency & Thermochemistry	ZPE, entropy, Gibbs energy	20 min

Analysis & Theory¶

Tutorial	Description	Time
Theoretical Framework	D-band analysis, BEP relations, energy span model	30 min
Microkinetic Modeling	TOF and steady-state analysis	35 min
Surface Comparison	Ranking catalysts with volcano plots	20 min

Advanced Topics¶

Tutorial	Description	Time
Doped Ceria (GDC/SDC/PDC)	Acceptor-doped ceria with O vacancies	25 min
Exsolution Simulation	Metal nanoparticle exsolution from perovskites	35 min
High-Throughput Screening	Systematic parameter scans	30 min
MACE ML Force Fields	Training and active learning	40 min

Workflow Diagrams¶

Complete NH3 Decomposition Study¶

┌─────────────────┐
│  Build Surface  │
│  from Bulk CIF  │
└────────┬────────┘
         │
         ▼
┌─────────────────┐
│ Create Defects  │
│ (O→N, vacancies)│
└────────┬────────┘
         │
         ▼
┌─────────────────┐
│  Place NH3      │
│  (6 methods)    │
└────────┬────────┘
         │
         ▼
┌─────────────────┐
│ Relax Structure │
│  (VASP/MACE)    │
└────────┬────────┘
         │
         ▼
┌─────────────────┐
│ Decomposition   │
│  Intermediates  │
│  NH2*, NH*, N*  │
└────────┬────────┘
         │
    ┌────┴────┐
    │         │
    ▼         ▼
┌───────┐ ┌────────┐
│  NEB  │ │  Freq  │
│  TS   │ │  ZPE   │
└───┬───┘ └───┬────┘
    │         │
    └────┬────┘
         │
         ▼
┌─────────────────┐
│    Analysis     │
│ • Energy profile│
│ • RDS/barriers  │
│ • Gibbs ΔG      │
│ • Microkinetics │
└─────────────────┘

Calculation Types¶

Calc Type	VASP INCAR	Purpose
`relax`	IBRION=2, NSW=300	Geometry optimization
`static`	NSW=0	Single-point energy
`frequency`	IBRION=5, NFREE=2	Vibrational modes
`neb`	IMAGES=5, LCLIMB=T	Transition states
`md`	IBRION=0, SMASS=0	Molecular dynamics

Best Practices¶

1. Start Simple¶

Begin with a small test system (2x2 surface)
Use lower ENCUT (400 eV) for initial tests
Verify convergence before production runs

2. Systematic Studies¶

Use consistent parameters across comparisons
Save all structures to database
Document calculation settings

3. Validation¶

Compare with literature values for benchmark systems
Check for imaginary frequencies after relaxation
Verify energy convergence with k-points and ENCUT

Example Scripts¶

All tutorials include complete, runnable code. Download example scripts:

# Clone with examples
git clone https://github.com/lizhenzhupearl/nh3sofc.git
cd NH3SOFC/examples

Video Tutorials¶

(Coming soon)