R
Name Radius
Section Mesh::Simulation Box
Type float
Defines the radius for BoxShape = sphere,
cylinder, or minimum. Must be a positive
number.
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 RashbaSpinOrbitCoupling
Section Hamiltonian
Type float
Default 0.0
(Experimental.) For systems described in 2D (electrons confined to 2D in semiconductor structures), one
may add the Bychkov-Rashba spin-orbit coupling term [Bychkov and Rashba, J. Phys. C: Solid
State Phys. 17, 6031 (1984)]. This variable determines the strength
of this perturbation, and has dimensions of energy times length.
Name RDMBasis
Section SCF::RDMFT
Type logical
Default yes
If true, all the energy terms and corresponding derivatives involved in RDMFT will
not be calculated on the grid but on the basis of the initial orbitals
Name RDMConvEner
Section SCF::RDMFT
Type float
Default 1e-6 Ha
Convergence criterion for stopping the overall minimization of the energy with
respect to occupation numbers and the orbitals. The minimization of the
energy stops when the total energy difference between two subsequent
minimizations of the energy with respect to the occupation numbers and the
orbitals is smaller than this criterion. It is also used to exit the orbital minimization.
Name RDMHartreeFock
Section SCF::RDMFT
Type logical
Default no
If true, the code simulates a HF calculation, by omitting the occ.num. optimization
can be used for test reasons
Name RDMTolerance
Section SCF::RDMFT
Type float
Default 1e-7 Ha
Convergence criterion for stopping the occupation numbers minimization. Minimization is
stopped when all derivatives of the energy wrt. each occupation number
are smaller than this criterion. The bisection for finding the correct mu that is needed
for the occupation number minimization also stops according to this criterion.
Name RDMToleranceFO
Section SCF::RDMFT
Type float
Default 1e-4 Ha
Convergence criterion for stopping the diagonalization of the Fock matrix in the Piris method.
Orbital minimization is stopped when all off-diagonal ellements of the Fock matrix
are smaller than this criterion.
Name RecalculateGSDuringEvolution
Section Time-Dependent::Propagation
Type logical
Default no
In order to calculate some information about the system along the
evolution (e.g. projection onto the ground-state KS determinant,
projection of the TDKS spin-orbitals onto the ground-state KS
spin-orbitals), the ground-state KS orbitals are needed. If the
ionic potential changes – that is, the ions move – one may want
to recalculate the ground state. You may do this by setting this
variable.
The recalculation is not done every time step, but only every
RestartWriteInterval time steps.
Name 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.
Name RegriddingInterpolationLevel
Section Mesh
Type integer
Default regridding_linear
Choose the interpolation order for the regridding. 0 is equivalent to nearest neighbor
interpolation. The default is linear interpolation.
Options:
- regridding_nearest_neighbor:
Use the nearest neighbor for the regridding. This is faster than the linear interpolation.
- regridding_linear:
Use a trilinear interpolation. This is implemented similar to restriction and prolongation
operations in multigrid methods. This ensures that both directions are adjoint to each other.
Name RegriddingRescale
Section Mesh
Type integer
Default scale_norm2
Rescale the regridded quantities. Not using a rescaling can lead to bad results if the
ratio of the grid spacings is large. The default is to rescale by the 2-norm of the quantity
except for generic interpolations (i.e. between curvilinear or non-commensurate grids).
Options:
- scale_none:
Do not rescale the regridded quantities.
- scale_norm2:
Scale the regridded quantities by the 2-norm of the quantity on the overlapping
region of the grid.
Name RegularizationFunction
Section Maxwell
Type integer
Default COS2
The current arising from charged point particles must be mapped onto the Maxwell
propagation grid. This requires a smearing or regularization function $\phi(\mathbf{r})$ attached to
each particle position $\mathbf{r}_i$ with user defined cutoff width, $\sigma$
Options:
- COS2:
$\phi(r)=\text{cos}^2(\frac{\pi}{2}\frac{|\mathbf{r}-\mathbf{r}_i|}{\sigma})$
if $|\mahtbf{r}-\mathbf{r}_i|<\sigma$, and 0 otherwise.
Name RegularizationFunctionWidth
Section Maxwell
Type float
Default 2
The current arising from charged point particles must be mapped onto the Maxwell
propagation grid. This requires a smearing or regularization function $\phi(\mathbf{r})$ attached to
each particle position $\mathbf{r}_i$ with user defined cutoff width, $\sigma$.
Default 2 bohrradii
Name RelativisticCorrection
Section Hamiltonian
Type integer
Default non_relativistic
The default value means that no relativistic correction is used. To
include spin-orbit coupling turn RelativisticCorrection to spin_orbit
(this will only work if SpinComponents has been set to non_collinear, which ensures
the use of spinors).
Options:
- non_relativistic:
No relativistic corrections.
- spin_orbit:
Spin-orbit.
- scalar_relativistic_zora:
scalar relativistic ZORA Hamiltonian
- fully_relativistic_zora:
fully relativistic spin-orbit ZORA Hamiltonian
including SR and SO terms
Name ReorderRanks
Section Execution::Parallelization
Type logical
Default no
This variable controls whether the ranks are reorganized to have a more
compact distribution with respect to domain parallelization which needs
to communicate most often. Depending on the system, this can improve
communication speeds.
Name ReportMemory
Section Execution::Debug
Type logical
Default no
If true, after each SCF iteration Octopus will print
information about the memory the code is using. The quantity
reported is an approximation to the size of the heap and
generally it is a lower bound to the actual memory Octopus is
using.
Name ResponseMethod
Section Linear Response
Type integer
Default sternheimer
Some response properties can be calculated either via
Sternheimer linear response or by using finite
differences. You can use this variable to select how you want
them to be calculated, it applies to em_resp and vib_modes
calculation modes. By default, the Sternheimer linear-response
technique is used.
Options:
- sternheimer:
The linear response is obtained by solving a self-consistent
Sternheimer equation for the variation of the orbitals. This
is the recommended method.
- finite_differences:
Properties are calculated as a finite-differences derivative of
the energy obtained by several ground-state calculations. This
method, slow and limited only to static response, is kept
mainly because it is simple and useful for testing purposes.
Name RestartFileFormatStates
Section Execution::IO
Type integer
Default obf
File format used for writing and reading the restart files for the states.
Default is obf.
Options:
- obf:
obf is the Octopus binary format, for which there is one file for
each state.
- adios2:
For large systems, especially with many k points, having one file per state can
be problematic for the file system. This option selects a format based on the
ADIOS2 library which needs to be available. The library handles IO efficiently
including aggregation and makes the restart IO much faster. However, it does
not support all features that the default obf format supports. Moreover, it
might use more memory for internal aggregation. In case of out-of-memory issues,
you might need to rerun on more nodes.
Name RestartFixedOccupations
Section States
Type logical
Default yes
Setting this variable will make the restart proceed as
if the occupations from the previous calculation had been set via the Occupations block,
i.e. fixed. Otherwise, occupations will be determined by smearing.
Name RestartOptions
Section Execution::IO
Type block
Octopus usually stores binary information, such as the wavefunctions, to be used
in subsequent calculations. The most common example is the ground-state states
that are used to start a time-dependent calculation. This variable allows to control
where this information is written to or read from. The format of this block is the following:
for each line, the first column indicates the type of data, the second column indicates
the path to the directory that should be used to read and write that restart information, and the
third column, which is optional, allows one to set some flags to modify the way how the data
is read or written. For example, if you are running a time-dependent calculation, you can
indicate where Octopus can find the ground-state information in the following way:
%RestartOptions
restart_gs | "gs_restart"
restart_td | "td_restart"
%
The second line of the above example also tells Octopus that the time-dependent restart data should be read from and written to the "td_restart" directory.
In case you want to change the path of all the restart directories, you can use the restart_all option. When using the restart_all option, it is still possible to have a different restart directory for specific data types. For example, when including the following block in your input file:
%RestartOptions
restart_all | "my_restart"
restart_td | "td_restart"
%
the time-dependent restart information will be stored in the "td_restart" directory, while all the remaining restart information will be stored in the "my_restart" directory.
By default, the name of the "restart_all" directory is set to "restart".
For multisystem calculations, the namespace of each system is inserted between the restart top folder and the specific
directory for each data type. When specifying a folder for a given system, the corresponding namespace is added
automatically to the folder name, unless the flag restart_literal is added.
Some CalculationModes also take into account specific flags set in the third column of the RestartOptions block. These are used to determine if some specific part of the restart data is to be taken into account or not when reading the restart information. For example, when restarting a ground-state calculation, one can set the restart_rho flags, so that the density used is not built from the saved wavefunctions, but is instead read from the restart directory. In this case, the block should look like this:
%RestartOptions
restart_gs | "restart" | restart_rho
%
A list of available flags is given below, but note that the code might ignore some of them, which will happen if they are not available for that particular calculation, or might assume some of them always present, which will happen in case they are mandatory.
Finally, note that all the restart information of a given data type is always stored in a subdirectory of the specified path. The name of this subdirectory is fixed and cannot be changed. For example, ground-state information will always be stored in a subdirectory named "gs". This makes it safe in most situations to use the same path for all the data types. The name of these subdirectories is indicated in the description of the data types below.
Currently, the available restart data types and flags are the following:
Options:
- restart_all:
(data type)
Option to globally change the path of all the restart information.
- restart_gs:
(data type)
The data resulting from a ground-state calculation.
This information is stored under the "gs" subdirectory.
- restart_unocc:
(data type)
The data resulting from an unoccupied states calculation. This information also corresponds to a ground state and
can be used as such, so it is stored under the same subdirectory as the one of restart_gs.
- restart_td:
(data type)
The data resulting from a real-time time-dependent calculation.
This information is stored under the "td" subdirectory.
- restart_em_resp:
(data type)
The data resulting from the calculation of the electromagnetic response using the Sternheimer approach.
This information is stored under the "em_resp" subdirectory.
- restart_em_resp_fd:
(data type)
The data resulting from the calculation of the electromagnetic response using finite-differences.
This information is stored under the "em_resp_fd" subdirectory.
- restart_kdotp:
(data type)
The data resulting from the calculation of effective masses by k.p perturbation theory.
This information is stored under the "kdotp" subdirectory.
- restart_vib_modes:
(data type)
The data resulting from the calculation of vibrational modes.
This information is stored under the "vib_modes" subdirectory.
- restart_vdw:
(data type)
The data resulting from the calculation of van der Waals coefficients.
This information is stored under the "vdw" subdirectory.
- restart_casida:
(data type)
The data resulting from a Casida calculation.
This information is stored under the "casida" subdirectory.
- restart_oct:
(data type)
The data for optimal control calculations.
This information is stored under the "opt-control" subdirectory.
- restart_partition:
(data type)
The data for the mesh partitioning.
This information is stored under the "partition" subdirectory.
- restart_proj:
(data type)
The ground-state to be used with the td_occup and populations options of TDOutput.
This information should be a ground state, so the "gs" subdirectory is used.
- restart_states:
(flag)
Read the electronic states. (not yet implemented)
- restart_rho:
(flag)
Read the electronic density.
- restart_vhxc:
(flag)
Read the Hartree and XC potentials.
- restart_mix:
(flag)
Read the SCF mixing information.
- restart_skip:
(flag)
This flag allows to selectively skip the reading and writing of specific restart information.
- restart_literal:
(flag)
Treat the given path literally, i.e. do not insert the namespace. This is useful for ensembles
if a given replica should read from a specific restart folder.
Name RestartReorderOccs
Section States
Type logical
Default no
Consider doing a ground-state calculation, and then restarting with new occupations set
with the Occupations block, in an attempt to populate the orbitals of the original
calculation. However, the eigenvalues may reorder as the density changes, in which case the
occupations will now be referring to different orbitals. Setting this variable to yes will
try to solve this issue when the restart data is being read, by reordering the occupations
according to the order of the expectation values of the restart wavefunctions.
Name RestartWallTimePeriod
Section Execution::IO
Type float
Default 120
Period Time (in minutes) at which the restart file will be written.
If a finite time (in minutes) is specified, the code will write the restart file every period.
Name RestartWithChangedGrid
Section Execution::IO
Type logical
Default false
Use restart data even when the grid has changed. Normally, this is not needed, but can be enabled.
Name RestartWrite
Section Execution::IO
Type logical
Default true
If this variable is set to no, restart information is not
written. Note that some run modes will ignore this
option and write some restart information anyway.
Name RestartWriteInterval
Section Execution::IO
Type integer
Default 50
Restart data is written when the iteration number is a multiple
of the RestartWriteInterval variable. For
time-dependent runs this includes the update of the output
controlled by the TDOutput variable. (Other output is
controlled by OutputInterval.)
Name RestartWriteTime
Section Execution::IO
Type float
Default 5
The RestartWriteTime (in minutes) will be subtracted from the WallTime to allow time for writing the restart file.
In huge calculations, this value should be increased.
Name RootSolver
Section Math::RootSolver
Type integer
Default root_newton
Specifies what kind of root solver will be used.
Options:
- root_newton:
Newton method.
Name RootSolverAbsTolerance
Section Math::RootSolver
Type float
Default 1e-10
Relative tolerance for the root-finding process.
Name RootSolverMaxIter
Section Math::RootSolver
Type integer
Default 500
In case of an iterative root solver, this variable determines the maximum number
of iteration steps.
Name RootSolverRelTolerance
Section Math::RootSolver
Type float
Default 1e-10
Relative tolerance for the root-finding process.