Octopus can run in 1, 2 or 3 dimensions, depending on the value of this variable (or more, if configured with –with-max-dim=4 or higher). Note that not all input variables may be available in all cases.
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:
interaction_type | interaction_mode | …
Here is an example to better understand how this works:
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:
Do not interact with any partner.
Interact with all available partners.
Interact only with some specified partners. A list of partner names must
Interact with all available partners except with some specified
partners. A list of partner names to exclude must be given.
Gravity interaction between two masses.
Lorentz force resulting from an EM field acting on a moving charge.
Coulomb force between two charged particles.
Linear medium for propagation of EM fields.
Drude dispersive linear medium for propagation of EM fields.
Electric field resulting from the Maxwell solver.
Force resulting from a Lennard Jones potential between classical particles.
Define how many directions are to be considered periodic. It has to be a number between zero and Dimensions.
No direction is periodic (molecule).
The x direction is periodic.
The x and y directions are periodic.
The x, y, and z directions are periodic.
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:
potential_user_defined | potential_formula | "1/2*r^2"
The potential is read from a file. Accepted file formats, detected by extension: obf, ncdf and csv.
Species with user-defined potential. The potential for the
species is defined by the formula given by the potential_formula
The potential for this species is created from the distribution
of charge given by the density_formula parameter.
The path for the file that describes the species.
Mathematical expression that defines the potential for species_user_defined. You can use
any of the x, y, z or r variables.
Mathematical expression that defines the charge density for species_charge_density. You can use
any of the x, y, z or r variables.
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.
An electronic system. (not fully implemented yet)
A maxwell system.
A classical particle. Used for testing purposes only.
A charged classical particle.
A DFTB+ system
A linear medium for classical electrodynamics.
A matter system containing electrons and classical ions.
(Experimental) A dispersive medium for classical electrodynamics.
A system containing other systems.