Elements

initialised -- logical

N -- integer

The number of atoms held

use_uniform_cutoff -- logical

Rather than covalent radii -- default is variable cutoff.

cutoff, cutoff_break -- real(dp)

if use_uniform_cutoff is true, cutoff is the cutoff distance in Å. Otherwise, cutoff is a multiplier for bond_length(Zi,Zj).

nneightol -- real(dp)

Count as nearest neighbour if sum of covalent radii times this%nneightol greater than distance between atoms. Used in cluster carving.

lattice -- real(dp), dimension(3,3)

Lattice vectors, as columns:

$$\left( \begin{array}{ccc} \vert & \vert & \vert \\ \mathbf{... ...} & R_{23} \\ R_{31} & R_{32} & R_{33} \\ \end{array}\right)$$

i.e. $\mathbf{a} =$ lattice(:,1), $\mathbf{b} =$ lattice(:,2) and $\mathbf{c} =$ lattice(:,3).

g -- real(dp), dimension(3,3)

Inverse lattice (stored for speed)

data -- type(Table)

This table contains all atomic data. Rows correspond to atoms, columns to the various properties.

properties -- type(Dictionary)

Mapping of names to column indices for the data table, e.g.

gives pos_indices = (/PROPERTY_REAL,1,3/), indicating that the position data consists of real number, beginning at column 1 and ending at column 3.

params -- type(Dictionary)

List of key/value pairs read from comment line of XYZ file

Z -- integer, pointer, dimension(:)

Atomic numbers, dimension is actually $(N)$

species -- character(TABLE_STRING_LENGTH), pointer, dimension(:)

Names of elements

move_mask -- integer, pointer, dimension(:)

Atoms with move_mask set to false are fixed

damp_mask -- integer, pointer, dimension(:)

Damping is only applied to those atoms with damp_mask set to 1. By default this is set to 1 for all atoms.

thermostat_region -- integer, pointer, dimension(:)

Which thermostat is applied to each atoms. By default this is set to 1 for all atoms.

travel -- integer, pointer, dimension(:,:)

Travel across periodic conditions. Actually $(3,N)$ array. See map_into_cell below.

pos -- real(dp), pointer, dimension(:,:)

$(3,N)$ array of atomic positions, in Å. Position of atom $i$ is pos(:,i)

mass -- real(dp), pointer, dimension(:)

Atomic masses, dimension is actually $(N)$

velo -- real(dp), pointer, dimension(:,:)

$(3,N)$ array of atomic velocities, in Å/fs.

acc -- real(dp), pointer, dimension(:,:)

$(3,N)$ array of accelerations in Å/fs$^2$

avgpos -- real(dp), pointer, dimension(:,:)

$(3,N)$ array of time-averaged atomic positions.

oldpos -- real(dp), pointer, dimension(:,:)

$(3,N)$ array of positions of atoms at previous time step.

avg_ke -- real(dp), pointer, dimension(:)

Time-averaged atomic kinetic energy

connect -- type(Connection)

Connectivity object (see above)

hysteretic_connect -- type(Connection)

Hysteretic connectivity object (see above)

initialise interface