[Smeagol-discuss] Fwd: error in transmission coefficient

[Garcia-Suarez, Victor]

Dear Prakash,

Have you checked that the coordinates at the beginning and the end of the coordinates block in the fdf file are exactly those of the bulk layers? A common mistake is to put at the end the coordinates of the molecule, which is not right.

Victor

-----Original Message-----
From: smeagol-discuss-bounces at lists.tchpc.tcd.ie on behalf of prakash parida
Sent: Wed 5/28/2008 05:51
To: smeagol-discuss at lists.tchpc.tcd.ie
Subject: [Smeagol-discuss] Fwd:  error in transmission coefficient
 
---------- Forwarded message ----------
From: prakash parida <prakash.friend at gmail.com>
Date: 2008/5/28
Subject: Re: [Smeagol-discuss] error in transmission coefficient
To: Ivan Rungger <runggeri at tcd.ie>


Dear smeagol users,
                                  Now the spins of lead and EM are matching
at the junction and also i used one kpoint along z direction. Now  problem
is  singular matrix . I  made TOLA, TOLB   to  10^(-15)  in gensvd.f , but
still the error persist.  like

out put file
.....................................................................

xijorb: WARNING: orbital pair      3   432 is multiply connected


InitMesh: MESH =   192 x   160 x   384 =    11796480
InitMesh: Mesh cutoff (required, used) =   400.000   415.396 Ry

* Maximum dynamic memory allocated =   135 MB
gensvd: Leads decimation
gensvd: Dim of H1 and S1 :    936
gensvd: Rank of H1:             0
gensvd: Rank of (H1,S1):        0
gensvd: Decimated states:     936
gensvd: Decimation from the left
gensvd: Leads decimation
gensvd: Dim of H1 and S1 :    936
gensvd: Rank of H1:             0
gensvd: Rank of (H1,S1):        0
gensvd: Decimated states:     936
gensvd: Decimation from the left
gensvd: Leads decimation
gensvd: Dim of H1 and S1 :    936
gensvd: Rank of H1:             0
gensvd: Rank of (H1,S1):        0
gensvd: Decimated states:     936
gensvd: Decimation from the left
gensvd: Leads decimation
gensvd: Dim of H1 and S1 :    936
gensvd: Rank of H1:             0
gensvd: Rank of (H1,S1):        0
gensvd: Decimated states:     936
gensvd: Decimation from the left
 The condition number of the matrix H1 was too large
 The Matrix is possibly singular
 (-2.718284846777614E-002,0.596902604260000)          15
 The condition number of the matrix H1 was too large
 The Matrix is possibly singular
.....................................................................................................................................................
 I could not understand  :
xijorb: WARNING: orbital pair      3   432 is multiply connected

could any body give any suggestion .

2008/5/26 Ivan Rungger <runggeri at tcd.ie>:

Dear Prakash,
>
>  the error indicates that you use a spin-polarized calculation in the
> extended molecule calculation, and a non-spin-polarized calculation in
> the leads (or the opposite). Both leads and extended molecule
> calculation have the same value for the "SpinPolarized" fdf option.
>
> By the way, the warning that you have indicates that you are using
> k-points along the transport direction in the extended molecule
> calculation, this is not necessary.
>
> Cheers,
>
>  Ivan
>
>
> prakash parida wrote:
> > Dear Smeagol Users,
> >                                    we are facing problem in
> > calculation of Transport  property  with graphene electrode .
> > programme is terminating with the following errors in out put files
> > and also i am attaching the necessary files
> >
> > output files
> >
> ...........................................................................................................................................................................
> > siesta:                 ===============================
> > SMEAGOL                 Bias step =    0, V =  0.000 Ry
> >                             Begin CG move =      0
> >                         ===============================
> >
> > iodm: Reading Density Matrix from files
> >
> > InitMesh: MESH =   180 x   160 x   384 =    11059200
> > InitMesh: Mesh cutoff (required, used) =   400.000   414.393 Ry
> >
> > * Maximum dynamic memory allocated =   337 MB
> > WARNING: There are k-points along z
> > ERROR: The spin at the left lead is not
> > the same as in the extended molecule
> >
> ............................................................................................................................................................................
> >
> >
> > could anybody help us out ,please .
> > --
> > PRAKASH PARIDA
> > PHD (THEORETICAL SCIENCE UNIT)
> > JNCASR,BANGALORE,INDIA
> > prakashp at jncasr.ac.in <mailto:prakashp at jncasr.ac.in>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Smeagol-discuss mailing list
> > Smeagol-discuss at lists.tchpc.tcd.ie
> > http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
>
>
> --
> =================================================
> Ivan Rungger,
>
> School of Physics and CRANN,
> Trinity College Dublin,
> Dublin 2,  IRELAND
> Phone: +353-1-8968454
> Email: runggeri at tcd.ie
> =================================================
>
>
>


-- 
PRAKASH PARIDA
PHD (THEORETICAL SCIENCE UNIT)
JNCASR,BANGALORE,INDIA
prakashp at jncasr.ac.in



-- 
PRAKASH PARIDA
PHD (THEORETICAL SCIENCE UNIT)
JNCASR,BANGALORE,INDIA
prakashp at jncasr.ac.in