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structure

Specify a molecular or periodic structure. This command can appear in the global context.

Subcommands

Options

bond_length

Sets the bond length for a diatomic formula:

structure(formula = HCl bond_length = 1.0 angstrom)
  • The type is quantity
  • There is no default value.
charges

Specify a map of modified nuclear charges for each element.

structure(
  molecule = water
  charges = {H: 1.0, O: 6.0})
  • The type is {real}
  • There is no default value.
dummy

Specify a list of dummy atoms, ordered according to the order in input (or in an external file), starting at 1. The charge of the dummy-atom nucleus is set to zero, and the default number of electrons is reduced by the atomic number. For example

structure(
molecule = water
dummy = [2, 3])
will dummy the 2 hydrogen atoms.

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

Specify an xyz file for reading xyz data.

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

Specify a molecule by chemical formula. For example, a single atom can be loaded:

structure(formula = He)
For a diatomic formula a bond length must also be specified:

structure(formula = HCl bond_length = 1.0 angstrom)
  • The type is string
  • There is no default value.
fractional

Specify atoms and their fractional coordinates in the primitive cell. For example:

structure(
  fractional = [[C, 0.0,  0.0,  0.0 ],
                [C, 0.25, 0.25, 0.25]]
  lattice(a = 3.57 angstrom
          bravais = fcc)
)
The option requires a list of tuples. Each tuple must have an element name and three coordinates (as fractions of the lattice vectors). It also requires the lattice subcommand.

  • The type is [(string, real, real, real)]
  • There is no default value.
load

Load a previously saved structure. For example

foo := structure(molecule = water)
structure(load = foo)
loads the structure saved with name foo.

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

Specify a map of modified nuclear masses (in atomic mass units) for each element.

structure(
  molecule = water
  masses = {H: 4.0})

This option is deprecated.

  • The type is {real}
  • There is no default value.
molecule

Specify a molecule name from entos data/molecules directory. For example:

structure(molecule = water)
loads a single water molecule.

  • The type is string
  • There is no default value.
  • The value must be one of:
    • ethene
    • methane
    • methanol
    • propane
    • toluene
    • water
name

Specify the name of a set of results.

This option is deprecated.

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

Specify atoms and their cartesian positions. For example:

structure(
  xyz = [ [O, 0.0,  0.0,       -0.06669620],
          [H, 0.0,  0.76075414, 0.52934657],
          [H, 0.0, -0.76075414, 0.52934657] ]
)
The option requires a list of tuples. Each tuple must have an element name and three coordinates (in Angstrom).

  • The type is [(string, real, real, real)]
  • There is no default value.