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Simulation Bodies

YASS provides two main types of simulation objects: Particle and Cell. Each serves different purposes in molecular simulations:

  • Particle: Represents individual atoms or particles
  • Cell: Represents periodic systems like crystals

Several xyz files of different molecules, small clusters and periodic cells can be found in the testing directory of the main repo. These can be used as dummy systems to play with while learning how to use YASS.

Particle Objects

The Particle type is the fundamental building block for molecular simulations. Each particle has:

  • Position vector (r)
  • Velocity vector (v)
  • Mass (m)
  • Chemical symbol (s)

Creating Particles

You can create particles in several ways:

using YetAnotherSimulationSuite

# Read from XYZ file
atoms = readSystem("molecule.xyz")

# Create manually
water::Vector{MyAtoms} = [
    Particle([0.000,  0.000, 0.000], zeros(3), 15.999, "O"),
    Particle([0.757,  0.586, 0.000], zeros(3),  1.008, "H"),
    Particle([0.757, -0.586, 0.000], zeros(3),  1.008, "H")
]

# Save to file
write("water.xyz", water)

Modifying Particles

The Particle type is mutable, allowing modifications after creation:

# Modify position
atoms[1].r .= [1.0, 0.0, 0.0]

# Change velocity
atoms[1].v .= [0.1, 0.0, 0.0]

# Update mass (e.g., for isotope studies)
atoms[1].m = 18.015  # Change to heavy water

# Change chemical symbol
atoms[1].s = "D"     # Deuterium

Particle Manipulation Functions

YASS provides several utility functions for working with particles:

# Translate all particles
translate!(atoms, [1.0, 0.0, 0.0])

# Center particles at origin
centerBdys!(atoms)

# Swap positions of two particles
swapAtoms!(atoms, 1, 2)

# Change isotopes for specific atoms
swapIso!(atoms, [1,2], [2.014, 2.014])  # Convert H to D

# Get center of mass
com = CoM(atoms)

# Get center of mass velocity
vcom = vCoM(atoms)

# Remove center of mass motion
zeroVCoM!(atoms)

Cell Objects

The Cell type represents periodic systems and contains:

  • Lattice matrix
  • Scaled positions (fractional coordinates)
  • Velocities
  • Masses
  • Chemical symbols
  • Periodic boundary conditions
  • Neighbor counts

Creating Cells

using YetAnotherSimulationSuite

# Read from file with lattice information
cell = readSystem("crystal.xyz")

# Create from atoms and lattice
atoms = [
    Particle([0.0, 0.0, 0.0], zeros(3), 22.990, "Na"),
    Particle([0.5, 0.5, 0.5], zeros(3), 35.450, "Cl")
]
lattice = [
    5.0 0.0 0.0
    0.0 5.0 0.0
    0.0 0.0 5.0
]
cell = makeCell(atoms, lattice)

# Specify periodic boundary conditions
cell = makeCell(atoms, lattice, 
    PBC=[true, true, true],  # Periodic in all directions
    NC=[1,1,1]               # Neighbor cells to consider
)

# Save cell to file
write("nacl.xyz", cell)

Cell Operations

YASS provides various functions for cell manipulation:

# Wrap atoms back into primary cell
wrap!(cell)

# Center atoms in cell
center!(cell)

# Create supercell
transform = [2 0 0; 0 2 0; 0 0 2]  # 2x2x2 supercell
super = makeSuperCell(cell, transform)

# Convert between cell and atoms
atoms = makeBdys(cell)        # Cell -> Atoms
cell = makeCell(atoms, lat)   # Atoms -> Cell

# Get Cartesian positions
positions = getPos(cell)

# Get cell volume
volume = getVolume(cell)

# Reorder atoms
order = sortperm([atom.m for atom in atoms])
reorder!(cell, order)