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'
)
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 coordinatesirc
- 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 output0
- Output that doesn't scale with system size1
- Output that scales linearly with system size2
- (Debugging) output that scales quadratically with system size3
- (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.