API Reference¶

Complete API documentation for the nh3sofc package.

Package Structure¶

nh3sofc/
├── core/           # Base classes and constants
├── structure/      # Structure building
├── calculators/    # VASP and MACE interfaces
├── jobs/           # HPC job management
├── workflows/      # Automated workflows
├── analysis/       # Post-processing tools
└── database/       # Data management

Modules¶

Core¶

Module	Description
`nh3sofc.core.constants`	Physical constants, default parameters
`nh3sofc.core.base`	Base classes for structures and workflows

Structure Building¶

Class	Description
`BulkStructure`	Load and manipulate bulk crystals
`SurfaceBuilder`	Create surface slabs
`DefectBuilder`	Create oxynitride defects
`AdsorbatePlacer`	Place adsorbate molecules
`DecompositionBuilder`	Generate decomposition intermediates

Calculators¶

Class	Description
`VASPInputGenerator`	Generate VASP input files
`VASPOutputParser`	Parse VASP results
`FrequencyCalculation`	Vibrational analysis
`MACECalculatorWrapper`	MACE ML force field

Workflows¶

Class	Description
`RelaxationWorkflow`	Geometry optimization
`DecompositionWorkflow`	NH3 decomposition pathway
`NEBWorkflow`	Transition state search
`FrequencyWorkflow`	Thermochemistry
`ScreeningWorkflow`	High-throughput screening

Analysis¶

Class	Description
`AdsorptionEnergyCalculator`	Adsorption energies
`HarmonicThermo`	Adsorbate thermodynamics
`RDSAnalyzer`	Rate-determining step
`SurfaceComparator`	Compare catalyst surfaces
`MicroKineticModel`	Microkinetic modeling

Database¶

Class	Description
`NamingConvention`	Standardized naming
`NH3SOFCDatabase`	ASE database wrapper

Quick Reference¶

Common Imports¶

# Structure
from nh3sofc.structure import (
    BulkStructure,
    SurfaceBuilder,
    DefectBuilder,
    AdsorbatePlacer,
    DecompositionBuilder,
)

# Calculators
from nh3sofc.calculators.vasp import (
    VASPInputGenerator,
    VASPOutputParser,
    FrequencyCalculation,
)
from nh3sofc.calculators.mace import (
    MACECalculatorWrapper,
    TrainingDataExtractor,
)

# Workflows
from nh3sofc.workflows import (
    RelaxationWorkflow,
    DecompositionWorkflow,
    NEBWorkflow,
    FrequencyWorkflow,
    ScreeningWorkflow,
)

# Analysis
from nh3sofc.analysis import (
    AdsorptionEnergyCalculator,
    HarmonicThermo,
    IdealGasThermo,
    RDSAnalyzer,
    SurfaceComparator,
    MicroKineticModel,
)

# Database
from nh3sofc.database import (
    NamingConvention,
    NH3SOFCDatabase,
)

Physical Constants¶

from nh3sofc.core.constants import (
    KB_EV,          # 8.617e-5 eV/K - Boltzmann constant
    H_EV_S,         # 4.136e-15 eV·s - Planck constant
    C_CMS,          # 2.998e10 cm/s - Speed of light
    EV_TO_J,        # 1.602e-19 J/eV - Energy conversion
    HUBBARD_U,      # Default Hubbard U values
    GAS_PHASE_ENERGIES,  # Reference gas energies
)

Default VASP Parameters¶

from nh3sofc.core.constants import DEFAULT_VASP_PARAMS

# Defaults:
# encut=520, ediff=1e-6, ediffg=-0.02
# ismear=0, sigma=0.05, kspacing=0.03
# ispin=2, lorbit=11, ncore=4