Name Dimensions
Section System
Type integer
Default 3

Octopus can run in 1, 2 or 3 or more dimensions, depending on the value of this variable. Note that not all input variables may be available in all cases.

Name InitialDisplacementAmplitudePos
Section System
Type float
Default 1.0

Amplitude for initial position displacement according to the phonon mode, defined by InitialDisplacementMode. The value corresponds to the normal distributed canonical coordinates.

Name InitialDisplacementAmplitudeVel
Section System
Type float
Default 1.0

Amplitude for initial velocity displacement according to the phonon mode, defined by InitialDisplacementMode. The value corresponds to the normal distributed canonical coordinates.

Name InitialDisplacementMode
Section System
Type integer
Default 0

When this variable is set and non-zero, the phonon modes file will be read, and ionic positions and velocities will be displaced according to a single phonon mode. The amplitudes can be defined with the variables:

• InitialDisplacementsAmplitudePos
• InitialDisplacementsAmplitudeVel
  
  

Name Interactions
Section System
Type block

This input option controls the interactions between systems. It basically allows to select which systems will interact with another system through a given interaction type. The format of the block is the following:

%Namespace.Interactions
  interaction_type | interaction_mode | …
%

Here is an example to better understand how this works:

%SystemA.Interactions
  gravity | all_except | "SystemB"
%

This means that SystemA and all the systems that belong to the same namespace (i.e., all its subsystems) will interact through gravity with all interaction partners that are also able to interact through gravity, except with SystemB. Note that the opposite is not true so, although clearly unphysical, this will not prevent SystemB from feeling the gravity from SystemA (in Octopus the interactions are always one-sided).

NB: Each interaction type should only appear once in the block. Any further instances beyond the first will be ignored.

Available modes and interaction types:

Options:

• no_partners:
  (interaction mode) Do not interact with any partner.
  
• all_partners:
  (interaction mode) Interact with all available partners.
  
• only_partners:
  (interaction mode) Interact only with some specified partners. A list of partner names must be given.
  
• all_except:
  (interaction mode) Interact with all available partners except with some specified partners. A list of partner names to exclude must be given.
  
• gravity:
  (interaction type) Gravity interaction between two masses.
  
• lorentz_force:
  (interaction type) Lorentz force resulting from an EM field acting on a moving charge.
  
• coulomb_force:
  (interaction type) Coulomb force between two charged particles.
  
• linear_medium_to_em_field:
  (interaction type) Linear medium for propagation of EM fields.
  
• current_to_mxll_field:
  (interaction type) Drude dispersive linear medium for propagation of EM fields.
  
• maxwell_e_field:
  (interaction type) Electric field resulting from the Maxwell solver.
  
• maxwell_b_field:
  (interaction type) Magnetic field resulting from the Maxwell solver.
  
• maxwell_vector_potential:
  (interaction type) Vector potential resulting from the Maxwell solver.
  
• lennard_jones:
  (interaction type) Force resulting from a Lennard Jones potential between classical particles.
  

Name NumberOfReplicas
Section System
Type integer
Default 1

Number of replicas to be created for the ensemble.

Name PeriodicDimensions
Section System
Type integer
Default 0

Define how many directions are to be considered periodic. It has to be a number between zero and Dimensions.

Options:

• 0:
  No direction is periodic (molecule).
  
• 1:
  The x direction is periodic.
  
• 2:
  The x and y directions are periodic.
  
• 3:
  The x, y, and z directions are periodic.
  

Name PhononModesFile
Section System
Type string

Filename for the phonon modes file. This file is in plain text with the following format: Version: # Version number (currently ignored) Nmodes: # Number of modes in the file Np: # Number of primitive cells in the supercell, used to generate the modes

frequency: # Frequency of first mode (in atomic units) # Normal mode eigenvector (for first atom) # Normal mode eigenvector (for second atom) … # repeated for all atoms in the unit cell frequency: # Frequency of second mode … Note that the order of atoms has to be the same as in the input (or geometry) file.

Name PhononModesZeroThreshold
Section System
Type float

Frequency threshold (in atomic units), below which phonon modes should be considered as zero frequency modes, such as translations or rotations, and be ignored for the generation of initial displacements.

Name StaticExternalPotentials
Section System
Type block

An static external potential is a model potential added to the local potential of the Hamiltonian

The format of this block is the following: The first field defines the type of species (the valid options are detailed below).

Then a list of parameters follows. The parameters are specified by a first field with the parameter name and the field that follows with the value of the parameter. Some parameters are specific to a certain species while others are accepted by all species. These are mass, max_spacing, and min_radius.

These are examples of possible species:

%ExternalPotential
   potential_user_defined | potential_formula | "1/2*r^2"
%

Options:

• potential_from_file:
  The potential is read from a file. Accepted file formats, detected by extension: obf, ncdf and csv.
  
• potential_user_defined:
  Species with user-defined potential. The potential for the species is defined by the formula given by the potential_formula parameter.
  
• potential_charge_density:
  The potential for this species is created from the distribution of charge given by the density_formula parameter.
  
• file:
  The path for the file that describes the species.
  
• potential_formula:
  Mathematical expression that defines the potential for species_user_defined. You can use any of the x, y, z or r variables.
  
• density_formula:
  Mathematical expression that defines the charge density for species_charge_density. You can use any of the x, y, z or r variables.
  

Name Systems
Section System
Type block

List of systems that will be treated in the calculation. The first column should be a string containing the system name. The second column should be the system type. See below for a list of available system types.

Options:

• electronic:
  An electronic system. (not fully implemented yet)
  
• maxwell:
  A maxwell system.
  
• classical_particle:
  A classical particle. Used for testing purposes only.
  
• charged_particle:
  A charged classical particle.
  
• dftbplus:
  A DFTB+ system
  
• linear_medium:
  A linear medium for classical electrodynamics.
  
• matter:
  A matter system containing electrons and classical ions.
  
• dispersive_medium:
  (Experimental) A dispersive medium for classical electrodynamics.
  
• multisystem:
  A system containing other systems.
  
• ions:
  An ensemble of classical charged particles.
  
• ensemble:
  An ensemble for multitrajectory runs