Phonons

Methods to calculate vibrations and e-ph couplings from SIESTA output

usage:

Phonons [-h] [-c] [-r] [–CheckPointNetCDF CHECKPOINTNETCDF] [-s] [-F DEVICEFIRST] [-L DEVICELAST] [–FCfirst FCFIRST] [–FClast FCLAST] [–EPHfirst EPHFIRST] [–EPHlast EPHLAST] [–PBCFirst PBCFIRST] [–PBCLast PBCLAST] [–FCwildcard FCWILDCARD] [–OSdir ONLYSDIR] [-a] [-i ISOTOPES] [-x K1] [-y K2] [-z K3] [-g] DestDir

positional arguments:

DestDir Destination directory

optional arguments:

-h, --help

show this help message and exit

-c, --CalcCoupl

Calculate e-ph couplings [default=False]

-r, --Restart

Restart from a previous run [default=False]

--CheckPointNetCDF CHECKPOINTNETCDF

Old NetCDF file used for restart [default=None]

-s, --SinglePrec

Calculate e-ph couplings using single precision arrays [default=False]

-F DEVICEFIRST, --DeviceFirst DEVICEFIRST

First device atom index (in the electronic basis) [default=1]

-L DEVICELAST, --DeviceLast DEVICELAST

Last device atom index (in the electronic basis) [default=1000]

--FCfirst FCFIRST

First FC atom index [default=1]

--FClast FCLAST

Last FC atom index [default=1000]

--EPHfirst EPHFIRST

First atom index for which the e-ph. couplings are evaluated [default=FCfirst]

--EPHlast EPHLAST

Last atom index for which the e-ph. couplings are evaluated [default=FClast]

--PBCFirst PBCFIRST

For eliminating interactions through periodic boundary conditions in z-direction [default=1]

--PBCLast PBCLAST

For eliminating interactions through periodic boundary conditions in z-direction [default=1000]

--FCwildcard FCWILDCARD

Wildcard for FC directories [default=./FC*]

--OSdir ONLYSDIR

Location of OnlyS directory [default=./OSrun]

-a, --AbsoluteEnergyReference

Use an absolute energy reference (Fermi energy of equilibrium structure) for displaced Hamiltonians (e.g., when eF is not well-defined) instead of the instantaneous Fermi energy for the displaced geometries, cf. Eq.(17) in PRB 75, 205413 (2007) [default=False]

-i ISOTOPES, --Isotopes ISOTOPES

String, formatted as a list [[i1,m1],…], where the mass of atom index i1 (SIESTA numbering) will be set to m1. Alternatively, the argument can be a file with the string [default=[]]

-x K1, --k1 K1

k-point along a1 where e-ph couplings are evaluated [0.0]

-y K2, --k2 K2

k-point along a2 where e-ph couplings are evaluated [0.0]

-z K3, --k3 K3

k-point along a3 where e-ph couplings are evaluated [0.0]

-g, --WriteGradients

Write real-space gradients dH/dR to NetCDF [default=False]