# 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(
n_images = 4
equivalent_atoms = [[4, 5, 6]]
save_coordinates = 'no_methyl_rotation.xyz'
)

This command can appear in the global context.

### 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.