According to your input, your system is isolated by 10 Angstroms vacuum in all three directions (the maximum fractional coordinates given are ca. 0.3, 0.65, and 0.2) and should be recognized by siesta as "molecule" (look for an output line like "siesta: System type = molecule").
The simplest and most direct way to analyse charge redistribution may be to use the Mulliken population analysis, i.e., option "WriteMullikenPop 1" in the input file .fdf. It gives total electron density per atom and also a decomposition into atomic orbitals. Regards, Ulrich. From: zkg03mjmk [mailto:[email protected]] To: [email protected] Sent: Mon, 01 Nov 2010 21:54:20 +0100 Subject: [SIESTA-L] problem with .TOCH and .VH > Hi everyone, > I try to use SIESTA to study the charge density distribution in an Al > nanowire under external electric field. I meet some problem and any opinion > on this point will be highly appreciated. > Since valence electron in mental is free to move, so I think by applying an > electric field, the nanowire should be readily polarized with charge > separation at the surface. > The lattice parameter been used is written down below and can be seen in > attached Fig.1. Both SaveTotalCharge and SaveElectrostaticPotential are set > as .true. > * > Question 1* > The manual says the electric field should be orthogonal to bulk direction. > Since I'm using a 1D structure (actually nanowire in a cubic cell with > lattice vectors much larger than nanowire itself), I think electric field > can be any direction right? * > Question 2* > I first tried electric field along the nanowire length axis: [0 0 **] V/Ang > When ** is less than 0.3, the .TOCH and .VH output files exist. However when > ** is larger than 0.3, the .TOCH and .VH do not exist. Does anyone know why? > Then I use electric file inclined to length axis at an angle of 45 [0 ** > **]V/Ang, the maximum ** which can render .TOCH and .VH is less than 0.1. > *Question 3* > I used Seis2xsf and Xcrysden to plot the total charge. However the result is > very different from what I thought. The total charge distribution changes > little by applying external electric field (can be seen in attached Fig2): > the electron distribute evenly around atoms, and no polarization is > observed. The result is pretty wired. I do not know if the result is > correct. > > > LatticeConstant 1.00 Ang > %block LatticeVectors > 14.096 0.000 0.000 > 0.000 28.435 0.000 > 0.000 0.000 12.048 > %endblock LatticeVectors > > AtomicCoordinatesFormat Fractional > %include "Al.pos" > > %block AtomicCoordinatesAndAtomicSpec > ies > 0.0000000000000003 0.0000000149011605 0.0000000000000003 1 > 0.1453114107443159 0.0000000149011604 0.1700167904088450 1 > 0.2906228214886309 0.0000000149011604 0.0000000000000002 1 > 0.0000000000000002 0.0720369276872211 0.1700167904088450 1 > 0.1453114107443149 0.0720369276872210 0.0000000000000002 1 > 0.2906228214886309 0.0720369276872210 0.1700167904088450 1 > 0.0000000000000001 0.1440738404732820 0.0000000000000003 1 > 0.1453114107443149 0.1440738404732820 0.1700167904088450 1 > 0.2906228214886309 0.1440738404732820 0.0000000000000000 1 > 0.0000000000000002 0.2161107532593430 0.1700167904088450 1 > 0.1453114107443149 0.2161107532593430 0.0000000000000003 1 > 0.2906228214886309 0.2161107532593430 0.1700167904088450 1 > 0.0000000000000001 0.2881476660454040 0.0000000000000003 1 > 0.1453114107443149 0.2881476660454040 0.1700167904088450 1 > 0.2906228214886309 0.2881476660454040 0.0000000000000001 1 > 0.0000000000000002 0.3601845788314660 0.1700167904088450 1 > 0.1453114107443149 0.3601845788314660 0.0000000000000001 1 > 0.2906228214886309 0.3601845788314660 0.1700167904088450 1 > 0.0000000000000001 0.4322214916175270 0.0000000000000004 1 > 0.1453114107443149 0.4322214916175270 0.1700167904088450 1 > 0.2906228214886309 0.4322214916175270 0.0000000000000001 1 > 0.0000000000000002 0.5042584044035871 0.1700167904088450 1 > 0.1453114107443149 0.5042584044035871 0.0000000000000002 1 > 0.2906228214886309 0.5042584044035871 0.1700167904088450 1 > 0.0000000000000001 0.5762953171896490 0.0000000000000004 1 > 0.1453114107443149 0.5762953171896490 0.1700167904088450 1 > 0.2906228214886309 0.5762953171896490 0.0000000000000001 1 > 0.0000000000000001 0.6483322299757101 0.1700167904088450 1 > 0.1453114107443149 0.6483322299757101 0.0000000000000000 1 > 0.2906228214886309 0.6483322299757101 0.170016790408845 1 > %endblock AtomicCoordinatesAndAtomicSpecies > --- Max-Planck-Institut für Eisenforschung GmbH Max-Planck-Straße 1 D-40237 Düsseldorf Handelsregister B 2533 Amtsgericht Düsseldorf Geschäftsführung Prof. Dr. Jörg Neugebauer Prof. Dr. Dierk Raabe Prof. Dr. Martin Stratmann Dipl.-Kfm. Herbert Wilk Ust.-Id.-Nr.: DE 11 93 58 514 Steuernummer: 105 5891 1000 -------------------------------------------------
