Linux commands

How to change a file's owner and group in Linux

Experimental techniques

The core-level spectra of C represents the 2p partical density of states above the Fermi level.

Graphene

Electron-hole symmetry with approximation of nearest-neighbor interactions only in graphene originates from the bipartite nature of the honeycomb lattice structure.

useful Resources

Octopus pseudopotential
Siesta Mailing List
Transiesta Tutorial
Siesta Post-processing tools
Band structure and Green's function codes
PHYS 824: Introduction to Nanophysics Wiki
virtual vault for pseudopotentials
Structure and Property of Titanium Dioxide

Journals on Condensed Matter Physics

Condensed Matter Physics on arxiv.org
Virtual Journals in Science & Technology
Physical Review Letters
Physical Review B

Inside the codes of siesta & transiesta

How to get the density matrix for siesta and transiesta?
siesta finds the density matrix by diagonalizing the Hamiltonian matrix, while transiesta makes use of the Green functions technique to obtain the density matrix.

siesta-3.0.rc2 is not working for transport calculation. I have not try if it works for band structure calculation.

I will use 2.0.2 version of siesta to do geometry optimization. After that use siesta-3.0b to do transport calculation.

Parallel compilation of siesta & transiesta

For siesta-2.0.2, run
./configure FC=gfortran –enable-mpi
make

For siesta-3.0, run
../Src/object_setup.sh
../Src/Configure FC=gfortran –enable-mpi

Sometimes the configure script can not find the location for libraries such lapack, blas, blacs, scalapack. The path of libraries should be specified explicitly as below:

BLAS_LIBS=-lblas
LAPACK_LIBS=-llapack
BLACS_LIBS=-L/usr/lib64/openmpi/lib -lmpiblacs -lmpiblacsCinit -lmpiblacsF77init
SCALAPACK_LIBS=-L/usr/lib64/scalapack-openmpi -lscalapack

Inside the code

How to get the density matrix for siesta and transiesta? siesta finds the density matrix by diagonalizing the Hamiltonian matrix, while transiesta makes use of the Green functions technique to obtain the density matrix.

Settings about transiesta calculation

The ElectronicTemperature could be set to zero meV.
The maximum value of TS.ComplexContour.NLine is 11
TS.ComplexContour.Emin should be just a little bit lower than the smallest eigenvalues.