Create A Crystal Structure

Create A Crystal Structure#

The Crystal class is the fundamental building block for representing crystal structures in jrystal. It contains essential attributes and derived properties that fully describe a crystal system.

Core Attributes#

  • charges: Atomic numbers of each atom

  • positions: Cartesian coordinates of atoms

  • cell_vectors: Unit cell vectors

  • spin: Number of unpaired electrons

  • symbol: Chemical symbols of atoms

Derived Properties#

  • scaled_positions: Fractional coordinates of atoms

  • vol: Unit cell volume

  • num_atom: Total number of atoms

  • num_electron: Total number of electrons

  • reciprocal_vectors: Reciprocal lattice vectors

  • A: Alias for cell_vectors

  • B: Alias for reciprocal_vectors

Note

All quantities in jrystal use atomic units:

  • Length: 1 Bohr = 0.529177 Å

  • Energy: 1 Hartree = 27.211 eV

Creating Crystal Structures#

There are three ways to create a crystal structure:

1. Direct Construction#

Create a crystal by directly specifying its attributes:

from jrystal import Crystal

crystal = Crystal(
    charges=[6, 6],  # Two carbon atoms
    positions=[[0, 0, 0], [1.5, 1.5, 1.5]],  # Positions in Bohr
    cell_vectors=[[3, 0, 0], [0, 3, 0], [0, 0, 3]],  # Cubic cell in Bohr
    spin=0  # No unpaired electrons
)
print(crystal)

2. From Structure Files#

Load a structure from common chemistry file formats:

crystal = Crystal.create_from_file("structure.xyz")

Note

File loading uses ASE’s IO capabilities. See supported formats in the ASE documentation.

3. From Chemical Symbols#

Create a crystal using chemical symbols and coordinates:

crystal = Crystal.create_from_symbols(
    symbols="C C",  # Two carbon atoms
    positions=[[0, 0, 0], [1.5, 1.5, 1.5]],  # In Bohr
    cell_vectors=[[3, 0, 0], [0, 3, 0], [0, 0, 3]]  # In Bohr
)

Note

jrysta.Crystal.create_from_symbols uses ASE’s Atoms class internally and assumes periodic boundary conditions in all directions. Specifying periodic boundary conditions in a single direction is not supported.

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