Configuration

allomorph allows you to override default constants such as element properties, nanoparticle diameters, shapes, and atomic distributions.

Configuration File

You can provide a configuration file in JSON, YAML, or TOML format to the CLI using the --config argument.

YAML Example (`config.yaml`)

# Global constants
VACUUM_THICKNESS: 50.0
RANDOM_DISTRIB_NO: 5

# Nanoparticle parameters
DIAMETER_LIST: [20, 30, 40]
SHAPE_LIST: ["OT", "TO", "SP", "MY_CUSTOM_CUBE"]
RATIO_LIST: [25, 50, 75]

# Custom shape definitions
CUSTOM_SHAPES:
  MY_CUSTOM_CUBE:
    builder: "FaceCenteredCubic"
    surfaces: [[1, 0, 0]]
    layers: [5]

# Element property dictionary
ELE_DICT:
  Cu:
    lc: {FCC: 3.61}
    radius: 1.28
    mass: 63.55
    rho: 8960
    m: 0.063546
    bulkE: 3.49
  Ag:
    lc: {FCC: 4.09}
    radius: 1.44
    mass: 107.87
    rho: 10490
    m: 0.107868
    bulkE: 2.95

JSON Example (`config.json`)

{
  "VACUUM_THICKNESS": 50.0,
  "RANDOM_DISTRIB_NO": 5,
  "DIAMETER_LIST": [20, 30, 40],
  "ELE_DICT": {
    "Cu": {
      "lc": {"FCC": 3.61},
      "radius": 1.28,
      "mass": 63.55,
      "rho": 8960,
      "m": 0.063546,
      "bulkE": 3.49
    }
  }
}

CLI Usage

Pass the configuration file to any allomorph command:

allomorph --config config.yaml init-struct --stage mnp

Python API

In Python, you can use update_constants or pass a custom ele_dict to the generation functions.

from allomorph.constants import update_constants, load_config

# Load and update globally
config = load_config("config.yaml")
update_constants(config)

# Or pass to specific functions
from allomorph.init_struct.gen_mnp import main as gen_mnp_main
gen_mnp_main(ele_dict=config["ELE_DICT"])

Custom Shapes

You can define custom nanoparticle shapes by adding them to the CUSTOM_SHAPES dictionary in your configuration and including their name in SHAPE_LIST.

Currently, custom shapes are built using the ase.cluster.cubic.FaceCenteredCubic builder. You can specify surfaces and layers.

CUSTOM_SHAPES:
  LARGE_CUBE:
    builder: "FaceCenteredCubic"
    surfaces: [[1, 0, 0]]
    layers: [10]

Parallel Generation

Structure generation (MNP, BNP, TNP) now automatically utilizes multiple CPU cores via the multiprocessing module to speed up the creation of large datasets. No extra configuration is needed.

Required Element Properties

When defining a custom element in ELE_DICT, the following keys are required:

Key	Description	Unit
`lc`	Lattice constants (must contain `FCC` entry)	Å
`radius`	Metallic radius	Å
`mass`	Atomic mass	g/mol
`rho`	Density (required for feature extraction)	kg/m³
`m`	Molar mass (required for feature extraction)	kg/mol
`bulkE`	Bulk cohesive energy (required for feature extraction)	eV/atom