AuH2

In the folder Inelastica/Examples/AuH2 you will find a folder L9.68 and a Python script AuH2-setup.py. The folder contains two subfolders

  • CGrun is a standard SIESTA geometry optimization run for a H2 molecule in a bridge configuration connected to 1D Au wires.

  • TSrun is a standard TranSIESTA setup with the H2 molecule between two semi-infinite Au leads.

In both cases the folder name L9.68 refers to an electrode separation (between fixed Au atoms) of 9.68 Ang.

To demonstrate the methods of Inelastica you can try to run the following jobs in the listed order.

geom2geom

Go into the L9.68/CGrun folder and try:

geom2geom RUN.fdf struct3.xyz -x 3 -y 2 -z 1

This will convert the geometry from the fdf format to an xyz file repeated 3x2x1 times. geom2geom can handle xyz, fdf, ANI, XV etc files.

The command:

geom2geom --help

tells you how to use the script.

CGrun

The first task is to stretch the geometry from L9.68 to a new electrode separation of 10.0 Ang (e.g., with a folder name L10.00).

To do this make sure that

CG = True
FC = False
OS = False
TS = False

in AuH2-setup.py. Now simply type

python AuH2-setup.py

and the script will

  • make a new L10.00/CGrun folder

  • read the L9.68/CGrun/Chain.XV geometry and stretch to 10.0 Ang

  • write RUN.pbs script and submit to queue

FCrun/OSrun

The next task is to perform finite displacements of a selected group of atoms to determine vibrational frequencies, modes, and e-ph couplings.

To do this make sure that

CG = False
FC = True
OS = True
TS = False

in AuH2-setup.py. Now simply type

python AuH2-setup.py

TSrun

To run TranSIESTA for the stretched wire geometry (L10.00) use

CG = False
FC = False
OS = False
TS = True

PHrun

To use the data from the FCrun/OSrun folders to determine the vibrational frequencies, modes, and e-ph couplings, you can execute on the command line:

Phonons -c -F 9 -L 14 --FCfirst=11 --FClast=12 PHrun

To learn about the different flags, try

Phonons -h

EigenChannels

Go into the TSrun folder:

EigenChannels EC

will create a new subdirectory EC and calculate the eigenchannel scattering states. They are saved in the macu file format which can be read by molekel (old version?). Other file formats may be specified with the –cube=… option, see EigenChannels --help. Support for more file formats can be found by downloading the last release. In addition, you will get .xmgr files that can be plotted in xmgrace. Also try:

EigenChannels --help

to find more options.

IETS calculations

Go into the TSrun folder:

Inelastica -F 10 -L 15 -p ../PHrun/Output.nc --LOEscale=0.0 INrun

will create a new subdirectory INrun and calculate the IETS spectra. The results are saved in a netCDF file which can be examined by the ncdump command or plotted in xmgrace (compiled with netCDF support).

To learn about the different flags, try

Inelastica -h

You can compare your results to this netCDF output file.