Specification of the system¶

System¶

The input of the initial structure can be given with the following key System. Apart from cases in which the system is retrieved by restarting a previous calculations this specification is always required.

System
{Atoms
Atom Coords
End}

{Charge NetQ}

{Lattice
Vectors
End}

{LatticeStrain
eps1 value
eps2 value
eps3 value
eps4 value
eps5 value
eps6 value
}

{FractionalCoords}

{AtomMasses
Atom Mass
End}
End


The System key accepts a set of sub-keys to specify various details of the chemical system under evaluation

Atoms

Specifies the geometry of the molecular system as a list of rows, one row per atom.

Atom
The name of an atom type. It must be the standard one- or two-characters symbol for the chemical element: H, He, Li, and so on.
Coords
This specifies the coordinates of the atom. The x, y, z values of the Cartesian coordinates are by default interpreted in Ångstrom.
Charge

The net charge of the molecule can be controlled with this optional sub-key. If this sub-key is omitted the net total charge of the molecule is by default zero.

NetQ
The net total charge of the molecule.
Lattice

Information about the periodicity of the system is given through this sub-key. Its presence is optional, and it implies a periodic system. The subsequent computation will therefore evaluate the system accordingly. A list of up to three vectors (one per row) for the cell must be specified.

Vector
Three floating point values defining the periodicity vector along a given direction. One, two, or three vectors can be specified (each on a different row) to express linear, planar or bulk periodicity, respectively. If one vector is specified, periodicity must develop along the x axis. If two vectors are specified, periodicity must develop along the xy plane. The unit is the same as in the Atoms section.
LatticeStrain

Allows the application of a strain tensor to the lattice. The values of eps1 to eps6 represent the unique elements of the strain tensor, as follows:

eps1  eps6  eps5
eps6  eps2  eps4
eps5  eps4  eps3

FractionalCoords
This optional keyword modifies how the Atoms coordinates are interpreted. When the keyword is present, coordinates will be interpreted as fractions of the periodicity lattice vectors, instead of absolute geometric positions in 3D space. Necessarily, the presence of this sub-key requires Lattice to be specified.
AtomMasses

The default atomic masses used in DFTB are taken from Nuclear Physics A 565, 1-65 (1993). The atomic masses of selected atom types can be redefined via the AtomMasses block key. The units of the atomic mass is unified atomic mass unit.

Example: Three different hydrogen isotopes:

Atoms
N         0.000000    0.000000    0.010272
H        -0.471582   -0.816803    0.407861
H.D       0.943163    0.000000    0.407861
H.T      -0.471582    0.816803    0.407861
End
AtomMasses
H.D 2.01410
H.T 3.01605
End


Units¶

The Units key is optional. It allows to specify different units for Length, Angle, and Time, in place of the default ones.

Units
{length    angstrom|bohr}