Velocities

Name PDBVelocities
Section System::Velocities
Type string

Like XYZVelocities but in PDB format, as in PDBCoordinates.

Name RandomVelocityTemp
Section System::Velocities
Type float
Default 0.0

If this variable is present, Octopus will assign random velocities to the atoms following a Boltzmann distribution with temperature given by RandomVelocityTemp (in degrees Kelvin). The seed for the random number generator can be modified by setting GSL_RNG_SEED environment variable.

Name Velocities
Section System::Velocities
Type block

If XYZVelocities, PDBVelocities, and XSFVelocities are not present, Octopus will try to fetch the initial atomic velocities from this block. If this block is not present, Octopus will set the initial velocities to zero. The format of this block can be illustrated by this example:

%Velocities
  ‘C’ | -1.7 | 0.0 | 0.0
  ‘O’ |  1.7 | 0.0 | 0.0
%

It describes one carbon and one oxygen moving at the relative velocity of 3.4 velocity units.

Note: It is important for the velocities to maintain the ordering in which the atoms were defined in the coordinates specifications.

Name XSFVelocities
Section System::Velocities
Type string

Like XYZVelocities but in XCrySDen format, as in XSFCoordinates.

Name XYZVelocities
Section System::Velocities
Type string

Octopus will try to read the starting velocities of the atoms from the XYZ file specified by the variable XYZVelocities. Note that you do not need to specify initial velocities if you are not going to perform ion dynamics; if you are going to allow the ions to move but the velocities are not specified, they are considered to be null. Note: It is important for the velocities to maintain the ordering in which the atoms were defined in the coordinates specifications.