Dimensions
Section: System
Type: integer
Default: 3
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.
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.
(WARNING: For systems that are periodic in 1D and 2D, interaction between ions is assumed to be periodic in 3D.
This affects the calculation of total energy and forces.)
Options:
Coordinates
Section: System::Coordinates
Type: block
If XYZCoordinates, PDBCoordinates, and XSFCoordinates were not found,
Octopus tries to read the coordinates for the atoms from the block Coordinates. The
format is quite straightforward:
%Coordinates
'C' | -0.56415 | 0.0 | 0.0 | no
'O' | 0.56415 | 0.0 | 0.0 | no
%
The first line defines a carbon atom at coordinates (-0.56415, 0.0, 0.0),
that is not allowed to move during dynamical simulations. The second line has
a similar meaning. This block obviously defines a carbon monoxide molecule, if the
input units are eV_Angstrom. The number of coordinates for each species
must be equal to the dimension of your space (generally 3).
Note that in this way it is possible to fix some of the atoms (this
is not possible when specifying the coordinates through a PDBCoordinates or
XYZCoordinates file). The last column is optional, and the default is yes.
It is always possible to fix all atoms using the MoveIons directive.
PDBClassical
Section: System::Coordinates
Type: string
If this variable is present, the program tries to read the atomic coordinates for classical atoms.
from the file specified by its value. The same as PDBCoordinates, except that the
classical charge colum must be present. The interaction from the
classical atoms is specified by ClassicalPotential, for QM/MM calculations.
Not available in periodic systems.
PDBCoordinates
Section: System::Coordinates
Type: string
If this variable is present, the program tries to read the atomic coordinates
from the file specified by its value. The PDB (Protein Data Bank)
format is quite complicated, and it goes
well beyond the scope of this manual. You can find a comprehensive
description here.
From the plethora of instructions defined in the PDB standard, Octopus
only reads two, ATOM and HETATOM. From these fields, it reads:
ReducedCoordinates
Section: System::Coordinates
Type: block
This block gives the atomic coordinates relative to the real
space unit cell. The format is the same as the
Coordinates block.
Note that in Octopus the origin of coordinates is in the center
of the cell, so the coordinates inside the cell are in the
range [-0.5, 0.5).
This block cannot be used with the minimum box shape.
XSFCoordinates
Section: System::Coordinates
Type: string
Another option besides PDB and XYZ coordinates formats is XSF, as defined
by the XCrySDen visualization program. Specify the filename with this variable.
PeriodicDimensions will be set based on the first line
(CRYSTAL, SLAB, POLYMER, or MOLECULE),
and Lsize will be set based on the lattice vectors, for compatible values of BoxShape.
The file should not contain ATOMS, CONVVEC, or PRIMCOORD.
NOTE: The coordinates are treated in the units specified by Units and/or UnitsInput.
XSFCoordinatesAnimStep
Section: System::Coordinates
Type: integer
Default: 1
If an animated file is given with XSFCoordinates, this variable selects which animation step
will be used. The PRIMVEC block must be written for each step.
XYZCoordinates
Section: System::Coordinates
Type: string
If PDBCoordinates is not present, the program reads the atomic coordinates from
the XYZ file specified by the variable XYZCoordinates -- in case this variable
is present. The XYZ format is very simple: The first line of the file has an integer
indicating the number of atoms. The second can contain comments that are simply ignored by
Octopus. Then there follows one line per atom, containing the chemical species and
the Cartesian coordinates of the atom.
WARNING: By default the coordinates are treated in the units
specified by Units and/or UnitsInput, which
means Octopus might expect xyz files to be in atomic units. If
you want the XYZ file to be read in Angstrom, as most codes do,
you can set the variable UnitsXYZFiles to
angstrom.
IonicInteraction
Section: System::Species
Type: block
This block defines the type of classical interaction between
ions. Each line represents the interaction between two types of
species. The first two columns contain the species names, the
next column is the type of interaction as defined below. The
next columns are the parameters for the interaction (if
any). Pairs not specified interact through Coulomb`s law.
Note: In most cases there is no need to specify this block,
since Coulomb interaction will be used by default.
Options:
PseudopotentialSet
Section: System::Species
Type: integer
Default: standard
Selects the set of pseudopotentials used by default for species
not defined in the Species block.
These sets of pseudopotentials come from different
sources. Octopus developers have not validated them. We include
them with the code for convenience of the users, but you are
expected to check the quality and suitability of the
pseudopotential for your application.
Options:
Species
Section: System::Species
Type: block
A species is by definition either an "ion" (nucleus + core electrons) described
through a pseudopotential, or a model potential.
Note that some sets of pseudopotentials are distributed with
the code. To use these pseudopotentials, you do not need to define them
explicitly in the Species block, as default parameters
are provided.
You can select the set for default pseudopotentials using the
PseudopotentialSet variable.
Additional pseudopotentials can be downloaded from the
octopus homepage or from other sources. Supported norm-conserving pseudopotential formats are
detected by the file extension: UPF (.upf), PSF (SIESTA, .psf), FHI (ABINIT 6, .fhi),
CPI (Fritz-Haber, .cpi), QSO (quantum-simulation.org, for Qbox, .xml),
HGH (Hartwigsen-Goedecker-Hutter, .hgh).
PSPIO format can also be used via species_pspio if that library is linked.
Note: pseudopotentials may only be used in 3D.
The format of this block is the following: The first field is a
string that defines the name of the species. The second 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:
%Species
'O' | species_pseudo | file | 'O.psf' | lmax | 1 | lloc | 1
'H' | species_pseudo | file | '../H.hgh'
'Xe' | species_pseudo | set | pseudojo_pbe_stringent
'C' | species_pseudo | file | "carbon.xml"
'jlm' | species_jellium | jellium_radius | 5.0
'rho' | species_charge_density | density_formula | "exp(-r/a)" | mass | 17.0 | valence | 6
'udf' | species_user_defined | potential_formula | "1/2*r^2" | valence | 8
'He_all' | species_full_delta
'H_all' | species_full_gaussian | gaussian_width | 0.2
'Li1D' | species_soft_coulomb | softening | 1.5 | valence | 3
%
Options:
SpeciesProjectorSphereThreshold
Section: System::Species
Type: float
Default: 0.001
The pseudopotentials may be composed of a local part, and a linear combination of nonlocal
operators. These nonlocal projectors have "projector" form, \( \left| v \right> \left< v \right| \)
(or, more generally speaking, \( \left| u \right> \left< v \right| \)).
These projectors are localized in real space -- that is, the function \(v\)
has a finite support around the nucleus. This region where the projectors are localized should
be small or else the computation time required to operate with them will be very large.
In practice, this localization is fixed by requiring the definition of the projectors to be
contained in a sphere of a certain radius. This radius is computed by making sure that the
absolute value of the projector functions, at points outside the localization sphere, is
below a certain threshold. This threshold is set by SpeciesProjectorSphereThreshold.
SpeciesTimeDependent
Section: System::Species
Type: logical
Default: no
When this variable is set, the potential defined in the block Species is calculated
and applied to the Hamiltonian at each time step. You must have at least one species_user_defined
type of species to use this.
SubSystemCoordinates
Section: System::Subsystems
Type: block
Lists the name of the subsystem, the coordinates and the rotation to apply uppon reading.
A subsystem can figure multiple times.
%SubSystemCoordinates
'name_1' | x | y | z | o_xy | o_xz | o_yz
'name_2' | x | y | z | o_xy
'name_2' | x | y | z
'name_3' | x
%
SubSystems
Section: System::Subsystems
Type: block
Lists the name, the subsystem type, the directory and the optional parameters to be used on the subsystem calculation.
%SubSystems
'name_1' | frozen | 'directory_1' | nearest
'name_2' | frozen | 'directory_2' | nearest
'name_3' | frozen | 'directory_2' | nearest
%
For frozen subsystems the optional parameter is the type of interpolation to use.
Options:
PDBVelocities
Section: System::Velocities
Type: string
Like XYZVelocities but in PDB format, as in PDBCoordinates.
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).
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.
XSFVelocities
Section: System::Velocities
Type: string
Like XYZVelocities but in XCrySDen format, as in XSFCoordinates.
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.