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initial_string

Create a set of images between the given structures:

initial_string(
  structure(formula = H2 bond_length = 1.0 bohr)
  structure(formula = H2 bond_length = 2.0 bohr)
  n_images = 4
  save_coordinates = 'h2_stretch.xyz'
)

Multi structures can be chained together:

initial_string(
  structure(formula = H2 bond_length = 1.0 bohr)
  structure(formula = H2 bond_length = 2.0 bohr)
  structure(formula = H2 bond_length = 4.0 bohr)
  n_images = 4
  save_coordinates = 'h2_stretch.xyz'
)

Equivalent atoms can be checked to find the shortest paths:

trans_4 := optimize(
  structure(molecule = methanol)
  xtb(model=gfn0)
  dihedral(atoms=[2,1,3,4] value = 180 degree)
)
trans_5 := optimize(
  structure(molecule = methanol)
  xtb(model=gfn0)
  dihedral(atoms=[2,1,3,5] value = 180 degree)
)
initial_string(
  structure(load = trans_4)
  structure(load = trans_5)
  n_images = 4
  equivalent_atoms = [[4, 5, 6]]
  save_coordinates = 'no_methyl_rotation.xyz'
)
This command can appear in the global context.

Subcommands

Options

coordinates

Coordinates to use for transformation.

  • The type is string-lowered
  • The default is irc
  • The value must be one of:
    • xyz - Use cartesian coordinates
    • irc - Use internal coordinates
equivalent_atoms

Symmetry equivalent atoms that are permuted

  • The type is [[int]]
  • There is no default value.
linear_angle_threshold

Angles greater than this value are treated as linear angles.

  • The type is quantity
  • The default is 175 degree
n_images

Number of new images created between successive pairs of structures. For example, if three initial structures are provided, and n_images = 2 the resulting string will contain 7 structures in total.

  • The type is int
  • There is no default value.
  • The value must be positive
print_level

Print level.

  • The type is int
  • There is no default value.
  • The value must be one of:
    • -2 - No output
    • -1 - Minimum output
    • 0 - Output that doesn't scale with system size
    • 1 - Output that scales linearly with system size
    • 2 - (Debugging) output that scales quadratically with system size
    • 3 - (Debugging) output that scales cubically with system size
save_coordinates

Specify name of the xyz file containing the coordinates from each step of the optimization.

  • The type is string
  • There is no default value.