box¶
This section specifies simulation cell boundaries and placement configurations.
Box Sizing Methods¶
Specify exactly one of the following methods for sizing the simulation cell:
Option A: Explicit Box Length
dimensions: 3
box_length: [20.0, 20.0, 20.0]
Option B: Target Volume Fraction
dimensions: 3
vol_frac: 0.1
vol_frac_mols: ["my_star"] # List of molecules included in the calculation
Option C: Target Area Fraction (for 2D Systems)
dimensions: 2
area_frac: 0.1
area_frac_mols: ["my_star"]
aspect_ratio: [1.0, 1.0] # (Optional) Aspect ratio of the box dimensions
Placement Styles¶
The placement specifications are defined directly inside the box configuration dictionary.
Placement Option A: Uniform Placement Style
Apply the same placement style to all molecules:
placement_style: "random" # Can be "random" or "simple_cubic"
Placement Option B: Mixed Placement Style
Assign specific molecules to different placement styles:
placement_style:
simple_cubic: ["my_star"]
random: ["other_mol"]
Placement Option C: Simple Cubic Lattice Spacing and Order
Customize lattice properties when using simple cubic placement:
placement_style: "simple_cubic"
placement_spacing: [2.0, 2.0, 2.0] # Spacing between lattice sites
placement_order: "random" # "random", "alternating", or ordered (default)
Placement Failures and Overlap Exceptions¶
Warning
If the system generator is unable to place all requested molecules/particles into the box without overlap (due to high density, a small box volume, or overlapping lattice sites in simple cubic placement), it will raise an Exception (e.g. “Unable to place <molecule> in the Simple Cubic lattice” or “Unable to place all particles randomly after <limit> attempts”).
To avoid these exceptions, you can:
Increase the box size or decrease the target volume/area fraction.
Adjust the
placement_spacingparameter for the simple cubic grid.Verify that molecule specifications and diameters do not conflict with the box volume.