[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Amal Yassin]

Hello
How to solve the Error of (arch.make) during the compilation of Siesta ?!

Please Help !!

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[veerpal kaur dhiman]

Dear siesta users

I need to install siesta in parallel on HPCC. But " sudo apt-get install
."  i.e. commands starting with sudo are not working in my HPCC account
because there is an error that you are not in pseudoers file so can't
install it in whole system. I will have to install siesta in my own account
of HPCC without sudo command. So how can i do that?

Please let me know.
I will be very thankful.

With regards
Veerpal Kaur.

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[veerpal kaur dhiman]

Dear siesta users

I need to install siesta in parallel on HPCC. But " sudo apt-get install
."  i.e. commands starting with sudo are not working in my HPCC account
because there is an error that you are not in pseudoers file so can't
install it in whole system. I will have to install siesta in my own account
of HPCC without sudo command. So can i do that?

Please let me know.
I will be very thankful.

With regards
Veerpal Kaur.

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[veerpal kaur dhiman]

hello sir,
I got only two columns in band.dat file one for k and another for E.
There is no column for spin.

I also tried this
gnubands -s 1 < .bands > band_up.dat
gnubands -s 2 < .bands > band_dn.dat

But i got the exactly same bands for up and down.

Where may be the problem ?
Please help.

Thank you


On 12/1/20, veerpal kaur dhiman  wrote:
> Thank u sir
> But i got  only two columns in bands file
>
>
> On Tue, 1 Dec 2020, 2:34 am Nick Papior,  wrote:
>
>> The spin index is the last value in each row.
>>
>> So everything is compressed as a flat file format.
>>
>> Alternatively you can do:
>>
>> gnubands -s 1 < .bands > band_up.dat
>> gnubands -s 2 < .bands > band_dn.dat
>>
>> to split them in two files.
>>
>> Den fre. 27. nov. 2020 kl. 22.00 skrev veerpal kaur dhiman <
>> v.veerpa...@gmail.com>:
>>
>>> Dear siesta users
>>>
>>> I have been trying to calculate the spin polarized band structure for my
>>> system.
>>> First of all i optimized my system with
>>> "variable cell' true
>>> num of cg steps 500 and
>>> spinpolarized option false
>>>
>>> then using the relaxed coordinates and relaxed lattice parameters and
>>> with options
>>>
>>> variable cell false
>>> num of cg steps 0
>>> spinpolarized option true
>>> %block DM.InitSpin
>>>  3   +2.0
>>> %endblock DM.InitSpin
>>>
>>> .bands file is calculated
>>>  where "3" is used for denoting the atom iron  Fe in my system in fdf
>>> file.
>>>
>>> then i converted .bands file into .dat file using
>>> gnubands <.bands| band.dat
>>>
>>> but i have got a single file for bands i am unable to separate the
>>> spin up and spin down bands how to get these? is there any mistake.
>>>
>>> please help if anyone can
>>>
>>> Thank you
>>> Veerpal Kaur.
>>>
>>> --
>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>> --
>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>
>

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[veerpal kaur dhiman]

Thank u sir
But i got  only two columns in bands file


On Tue, 1 Dec 2020, 2:34 am Nick Papior,  wrote:

> The spin index is the last value in each row.
>
> So everything is compressed as a flat file format.
>
> Alternatively you can do:
>
> gnubands -s 1 < .bands > band_up.dat
> gnubands -s 2 < .bands > band_dn.dat
>
> to split them in two files.
>
> Den fre. 27. nov. 2020 kl. 22.00 skrev veerpal kaur dhiman <
> v.veerpa...@gmail.com>:
>
>> Dear siesta users
>>
>> I have been trying to calculate the spin polarized band structure for my
>> system.
>> First of all i optimized my system with
>> "variable cell' true
>> num of cg steps 500 and
>> spinpolarized option false
>>
>> then using the relaxed coordinates and relaxed lattice parameters and
>> with options
>>
>> variable cell false
>> num of cg steps 0
>> spinpolarized option true
>> %block DM.InitSpin
>>  3   +2.0
>> %endblock DM.InitSpin
>>
>> .bands file is calculated
>>  where "3" is used for denoting the atom iron  Fe in my system in fdf
>> file.
>>
>> then i converted .bands file into .dat file using
>> gnubands <.bands| band.dat
>>
>> but i have got a single file for bands i am unable to separate the
>> spin up and spin down bands how to get these? is there any mistake.
>>
>> please help if anyone can
>>
>> Thank you
>> Veerpal Kaur.
>>
>> --
>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>
>
>
> --
> Kind regards Nick
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

The spin index is the last value in each row.

So everything is compressed as a flat file format.

Alternatively you can do:

gnubands -s 1 < .bands > band_up.dat
gnubands -s 2 < .bands > band_dn.dat

to split them in two files.

Den fre. 27. nov. 2020 kl. 22.00 skrev veerpal kaur dhiman <
v.veerpa...@gmail.com>:

> Dear siesta users
>
> I have been trying to calculate the spin polarized band structure for my
> system.
> First of all i optimized my system with
> "variable cell' true
> num of cg steps 500 and
> spinpolarized option false
>
> then using the relaxed coordinates and relaxed lattice parameters and
> with options
>
> variable cell false
> num of cg steps 0
> spinpolarized option true
> %block DM.InitSpin
>  3   +2.0
> %endblock DM.InitSpin
>
> .bands file is calculated
>  where "3" is used for denoting the atom iron  Fe in my system in fdf file.
>
> then i converted .bands file into .dat file using
> gnubands <.bands| band.dat
>
> but i have got a single file for bands i am unable to separate the
> spin up and spin down bands how to get these? is there any mistake.
>
> please help if anyone can
>
> Thank you
> Veerpal Kaur.
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 
Kind regards Nick

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[veerpal kaur dhiman]

Dear siesta users

I have been trying to calculate the spin polarized band structure for my system.
First of all i optimized my system with
"variable cell' true
num of cg steps 500 and
spinpolarized option false

then using the relaxed coordinates and relaxed lattice parameters and
with options

variable cell false
num of cg steps 0
spinpolarized option true
%block DM.InitSpin
 3   +2.0
%endblock DM.InitSpin

.bands file is calculated
 where "3" is used for denoting the atom iron  Fe in my system in fdf file.

then i converted .bands file into .dat file using
gnubands <.bands| band.dat

but i have got a single file for bands i am unable to separate the
spin up and spin down bands how to get these? is there any mistake.

please help if anyone can

Thank you
Veerpal Kaur.

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[rayan moukhadder]

Dear siesta users,
I performed several transiesta runs with the leads  being parallel to each
other, now if I want to perform another calculation where the leads should
be antiparallel to each other what new conditions should be added to the
input file of the leads? In another words what are the condition that allow
me to perform a spin up calculation for the lead? and another spin down
calculation for the same lead?

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[alok karn]

i have an issue about the disappearing Atoms in bulk structure after
relaxing, i attach my relax.fdf right


relax.fdf
Description: Binary data

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[rayan moukhadder]

Hello everybody, after a successful siesta run a PDOS file is created, then
using fmpdos package to get the projected density of state plot , i got the
following error
Unknown Identifier in PDOS file line
SystemName armchair graphene
Can anyone please help me to  fix such a problem.
Thanks for your time.
Rayan Moukhader,
Lebanese University-Department of physics

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[El-abed Haidar]

But also take into account Nick’s comment on contour and used atoms.
Also you might be careful on the cutoff energy maybe for your system 150 Ry 
could be enough.
But a convergence test would be more suitable first.
Good luck!

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder<mailto:rayanroro321...@gmail.com>
Sent: Wednesday, 17 June 2020 6:15 AM
To: siesta-l@uam.es<mailto:siesta-l@uam.es>
Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Transport is along the z-direction, thanks for your help I will try to make use 
of those options.

‫في الاثنين، 15 يونيو 2020 في 11:02 م تمت كتابة ما يلي بواسطة ‪El-abed Haidar‏ 
<‪ehai2...@uni.sydney.edu.au<mailto:ehai2...@uni.sydney.edu.au>‏>:
Hi Rayan
Quick question what is the transport direction?
I feel there are some essential blocks missing. Those are generally required 
for a TranSIESTA and TbTrans calculation. Good luck!

%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
  mu V/2
  contour.eq
begin
  c-Left
  t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
begin
  c-Right
  t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ./left.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
  used-atoms 63
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ./right.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
  used-atoms 63
%endblock TS.Elec.Right
TS.Contours.Eq.Pole2.5 eV
%block TS.Contour.c-Left
  part circle
   from -999.99893 eV + V/2 to -10. kT + V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from -999.99893 eV - V/2 to -10. kT - V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta0.000100 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
 method mid-rule
%endblock TS.Contour.nEq.neq
# TBtrans options
TBT.T.Eig 5
TBT.Elecs.Eta0.136058 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from   -2.0 eV to2.0 eV
delta0.00800 eV
 method mid-rule
%endblock TBT.Contour.neq

TBT.DOS.A.All  true
TBT.CDF.MPI true
TS.Voltage 0.0 eV


El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder<mailto:rayanroro321...@gmail.com>
Sent: Monday, 15 June 2020 6:04 AM
To: siesta-l@uam.es<mailto:siesta-l@uam.es>
Subject: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Dear all,

I am a phd student and I am new to siesta , I am doing a Transiesta calculation 
for a system that consist of two graphene sheets sandwiching three cobalt 
atoms, as the electrode calculation is successfully done, the SCF iterations in 
SR calculation are not converging where my input file is

SystemName  SR.Co
SystemLabel SR.Co

NumberOfAtoms   131
NumberOfSpecies2

%block ChemicalSpeciesLabel
  1   6  C
  2   27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize  SZP
PAO.EnergyShift  0.05 Ry
PAO.SplitNorm0.2

==
==
# K-points

%block kgrid_Monkhorst_Pack
   1   0   0  0.0
   0   1   0  0.0
   0   0   1  0.5
%endblock Kgrid_Monkhorst_Pack
==
==
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL
LatticeConstant 1.00 Ang

%block LatticeVectors
17.016 0.000 0.000
0.000 9.824 0.000
0.000 0. 14.000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies

0.000 0.000 0.000 1
1.418 0.000 0.000 1
2.127 1.228 0.000 1
3.545 1.228 0.000 1
4.254 0.000 0.000 1
5.672 0.000 0.000 1
6.381  1.228 0.000 1
7.799  1.228 0.000 1
8.508  0.000 0.000 1
9.926  0.000 0.000 1
10.635 1.228 0.000 1
12.053 1.228 0.000 1
12.762 0.000 0.000 1
14.180 0.000 0.000 1
14.889 1.228 0.000 1
16.304 1.228 0.000 1
0.000  2.456 0.000 1
1.418  2.456 0.000 1
2.127  3.684 0.000 1
3.545  3.684 0.000 1
4.254  2.456 0.000 1
5.672  2.456 0.000 1
6.381  3.684 0.000 1
7.799  3.684 0.000 1
8.508  2.456 0.000 1
9.926  2.456 0.000 1
10.635 3.684 0.000 1
12.053 3.684 0.000 1
12.762 2.456 0.000 1
14.180 2.456 0.000 1
14.889 3.684 0.000 1
16.30

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[El-abed Haidar]

Thank you very much Nick!
No wonder my calculations were taking that much long!
El-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: Nick Papior<mailto:nickpap...@gmail.com>
Sent: Tuesday, 16 June 2020 4:41 PM
To: siesta-l<mailto:siesta-l@uam.es>; El-abed 
Haidar<mailto:ehai2...@uni.sydney.edu.au>
Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Hi,

1. Original poster. Could you please try read the manual. Your problem are 
multiple, the electronic structure parameters are insufficient and you are not 
using the electrodes as they should. I.e. they are not bulk like.

Your simulation requires the use of real-space self-energies, see 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417<https://protect-au.mimecast.com/s/Ty4RC91WPRTZl1JQcoJX1f?domain=journals.aps.org>
 .
However, if you are a first in doing transiesta/tbtrans calculations you should 
not start with something this complicated... :(

2. @El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au>, a comment on the input 
suggested.
   from -999.99893 eV - V/2 to -10. kT - V/2
Don't do this! You should probably never go below -100 eV, the default -40 eV 
should be sufficient for most systems, but -1000 eV is definitely too much.
Also, "used-atoms 63" should only be supplied in case you have a subset 
electrode calculation. Otherwise remove this line.

/ Nick

Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar 
mailto:ehai2...@uni.sydney.edu.au>>:
Hi Rayan
Quick question what is the transport direction?
I feel there are some essential blocks missing. Those are generally required 
for a TranSIESTA and TbTrans calculation. Good luck!

%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
  mu V/2
  contour.eq
begin
  c-Left
  t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
begin
  c-Right
  t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ./left.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
  used-atoms 63
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ./right.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
  used-atoms 63
%endblock TS.Elec.Right
TS.Contours.Eq.Pole2.5 eV
%block TS.Contour.c-Left
  part circle
   from -999.99893 eV + V/2 to -10. kT + V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from -999.99893 eV - V/2 to -10. kT - V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta0.000100 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
 method mid-rule
%endblock TS.Contour.nEq.neq
# TBtrans options
TBT.T.Eig 5
TBT.Elecs.Eta0.136058 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from   -2.0 eV to2.0 eV
delta0.00800 eV
 method mid-rule
%endblock TBT.Contour.neq

TBT.DOS.A.All  true
TBT.CDF.MPI true
TS.Voltage 0.0 eV


El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder<mailto:rayanroro321...@gmail.com>
Sent: Monday, 15 June 2020 6:04 AM
To: siesta-l@uam.es<mailto:siesta-l@uam.es>
Subject: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Dear all,

I am a phd student and I am new to siesta , I am doing a Transiesta calculation 
for a system that consist of two graphene sheets sandwiching three cobalt 
atoms, as the electrode calculation is successfully done, the SCF iterations in 
SR calculation are not converging where my input file is

SystemName  SR.Co
SystemLabel SR.Co

NumberOfAtoms   131
NumberOfSpecies2

%block ChemicalSpeciesLabel
  1   6  C
  2   27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize  SZP
PAO.EnergyShift  0.05 Ry
PAO.SplitNorm0.2

==
==
# K-points

%block kgrid_Monkhorst_Pack
   1   0   0  0.0
   0   1   0  0.0
   0   0   1  0.5
%endblock Kgrid_Monkhorst_Pack
==
==
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL
LatticeConstant 1.00 Ang

%block LatticeVectors
17.016 0.000 0.000
0.000 9.824 0.000
0.000 0.00

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

A bulk system where you know the LDA+U results, then do the same bulk
system with NEGF + LDA+U.

Den tir. 16. jun. 2020 kl. 15.42 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:

> What should I be looking for? Because as far I have been aware of it has
> been highly recommended to utilize both simultaneously.
>
> My question in other words: What should I test exactly? U and J did you
> mean?
>
> Thank you and really appreciate your time!
>
> EL-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
>
> *From: *Nick Papior 
> *Sent: *Tuesday, 16 June 2020 11:35 PM
> *To: *El-abed Haidar 
> *Cc: *siesta-l 
> *Subject: *Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
>
>
>
> I have never tried, I don't know if there are any restrictions using both
> simultaneously. :(
>
>
>
> So a careful test of everything to see if it behaves as expected would be
> required, I think. ;)
>
>
>
> Den tir. 16. jun. 2020 kl. 15.32 skrev El-abed Haidar <
> ehai2...@uni.sydney.edu.au>:
>
> Thank you again Nick! Just a follow up question are we allowed to use
> LDA+U in TranSIESTA + TbTrans?
>
> Is that applicable? Has anyone published or tested such exchange
> correlation for current voltage calculations? Any further comments would be
> highly appreciated!
>
> Thank you and looking forward to your thoughts!
>
> EL-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
>
> *From: *El-abed Haidar 
> *Sent: *Tuesday, 16 June 2020 10:43 PM
> *To: *Nick Papior ; siesta-l 
> *Subject: *RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
>
>
>
> Thank you very much Nick!
>
> No wonder my calculations were taking that much long!
>
> El-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
>
> *From: *Nick Papior 
> *Sent: *Tuesday, 16 June 2020 4:41 PM
> *To: *siesta-l ; El-abed Haidar
> 
> *Subject: *Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
>
>
>
> Hi,
>
>
>
> 1. Original poster. Could you please try read the manual. Your problem are
> multiple, the electronic structure parameters are insufficient and you are
> not using the electrodes as they should. I.e. they are not bulk like.
>
>
>
> Your simulation requires the use of real-space self-energies, see
> https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417
> <https://protect-au.mimecast.com/s/6sxiCJyBrGf4jNBZCVeMd9?domain=journals.aps.org>
>  .
>
> However, if you are a first in doing transiesta/tbtrans calculations you
> should not start with something this complicated... :(
>
>
>
> 2. @El-abed Haidar , a comment on the input
> suggested.
>
>from -999.99893 eV - V/2 to -10. kT - V/2
>
> Don't do this! You should probably never go below -100 eV, the default -40
> eV should be sufficient for most systems, but -1000 eV is definitely too
> much.
>
> Also, "used-atoms 63" should only be supplied in case you have a subset
> electrode calculation. Otherwise remove this line.
>
>
>
> / Nick
>
>
>
> Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar <
> ehai2...@uni.sydney.edu.au>:
>
> Hi Rayan
>
> Quick question what is the transport direction?
>
> I feel there are some essential blocks missing. Those are generally
> required for a TranSIESTA and TbTrans calculation. Good luck!
>
>
>
> %block TS.ChemPots
>
>   Left
>
>   Right
>
> %endblock TS.ChemPots
>
> %block TS.ChemPot.Left
>
>   mu V/2
>
>   contour.eq
>
> begin
>
>   c-Left
>
>   t-Left
>
> end
>
> %endblock TS.ChemPot.Left
>
> %block TS.ChemPot.Right
>
>   mu -V/2
>
>   contour.eq
>
> begin
>
>   c-Right
>
>   t-Right
>
> end
>
> %endblock TS.ChemPot.Right
>
> TS.Elecs.Bulk true
>
> TS.Elecs.DM.Update cross-terms
>
> TS.Elecs.GF.ReUse true
>
> %block TS.Elecs
>
>   Left
>
>   Right
>
> %endblock TS.Elecs
>
> %block TS.Elec.Left
>
>   HS ./left.TSHS
>
>   chem-pot Left
>
>   semi-inf-dir -a2
>
>   elec-pos begin 1
>
>   used-atoms 63
>
> %endblock TS.Elec.Left
>
> %block TS.Elec.Right
>
>   HS ./right.TSHS
>
>   chem-pot Rig

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

Hi,

1. Original poster. Could you please try read the manual. Your problem are
multiple, the electronic structure parameters are insufficient and you are
not using the electrodes as they should. I.e. they are not bulk like.

Your simulation requires the use of real-space self-energies, see
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417 .
However, if you are a first in doing transiesta/tbtrans calculations you
should not start with something this complicated... :(

2. @El-abed Haidar , a comment on the input
suggested.

   from -999.99893 eV - V/2 to -10. kT - V/2
Don't do this! You should probably never go below -100 eV, the default -40
eV should be sufficient for most systems, but -1000 eV is definitely too
much.
Also, "used-atoms 63" should only be supplied in case you have a subset
electrode calculation. Otherwise remove this line.

/ Nick

Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:

> Hi Rayan
>
> Quick question what is the transport direction?
>
> I feel there are some essential blocks missing. Those are generally
> required for a TranSIESTA and TbTrans calculation. Good luck!
>
>
>
> %block TS.ChemPots
>
>   Left
>
>   Right
>
> %endblock TS.ChemPots
>
> %block TS.ChemPot.Left
>
>   mu V/2
>
>   contour.eq
>
> begin
>
>   c-Left
>
>   t-Left
>
> end
>
> %endblock TS.ChemPot.Left
>
> %block TS.ChemPot.Right
>
>   mu -V/2
>
>   contour.eq
>
> begin
>
>   c-Right
>
>   t-Right
>
> end
>
> %endblock TS.ChemPot.Right
>
> TS.Elecs.Bulk true
>
> TS.Elecs.DM.Update cross-terms
>
> TS.Elecs.GF.ReUse true
>
> %block TS.Elecs
>
>   Left
>
>   Right
>
> %endblock TS.Elecs
>
> %block TS.Elec.Left
>
>   HS ./left.TSHS
>
>   chem-pot Left
>
>   semi-inf-dir -a2
>
>   elec-pos begin 1
>
>   used-atoms 63
>
> %endblock TS.Elec.Left
>
> %block TS.Elec.Right
>
>   HS ./right.TSHS
>
>   chem-pot Right
>
>   semi-inf-dir +a2
>
>   elec-pos end -1
>
>   used-atoms 63
>
> %endblock TS.Elec.Right
>
> TS.Contours.Eq.Pole2.5 eV
>
> %block TS.Contour.c-Left
>
>   part circle
>
>from -999.99893 eV + V/2 to -10. kT + V/2
>
> points 50
>
>  method g-legendre
>
> %endblock TS.Contour.c-Left
>
> %block TS.Contour.t-Left
>
>   part tail
>
>from prev to inf
>
> points 10
>
>  method g-fermi
>
> %endblock TS.Contour.t-Left
>
> %block TS.Contour.c-Right
>
>   part circle
>
>from -999.99893 eV - V/2 to -10. kT - V/2
>
> points 50
>
>  method g-legendre
>
> %endblock TS.Contour.c-Right
>
> %block TS.Contour.t-Right
>
>   part tail
>
>from prev to inf
>
> points 10
>
>  method g-fermi
>
> %endblock TS.Contour.t-Right
>
> TS.Elecs.Eta0.000100 eV
>
> %block TS.Contours.nEq
>
>   neq
>
> %endblock TS.Contours.nEq
>
> %block TS.Contour.nEq.neq
>
>   part line
>
>from -|V|/2 - 5 kT to |V|/2 + 5 kT
>
> delta 0.01 eV
>
>  method mid-rule
>
> %endblock TS.Contour.nEq.neq
>
> # TBtrans options
>
> TBT.T.Eig 5
>
> TBT.Elecs.Eta0.136058 eV
>
> %block TBT.Contours
>
>   neq
>
> %endblock TBT.Contours
>
> %block TBT.Contour.neq
>
>   part line
>
>from   -2.0 eV to2.0 eV
>
> delta0.00800 eV
>
>  method mid-rule
>
> %endblock TBT.Contour.neq
>
>
>
> TBT.DOS.A.All  true
>
> TBT.CDF.MPI true
>
> TS.Voltage 0.0 eV
>
>
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
>
> *From: *rayan moukhadder 
> *Sent: *Monday, 15 June 2020 6:04 AM
> *To: *siesta-l@uam.es
> *Subject: *[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
>
>
>
> Dear all,
>
>
>
> I am a phd student and I am new to siesta , I am doing a Transiesta
> calculation for a system that consist of two graphene sheets sandwiching
> three cobalt atoms, as the electrode calculation is successfully done, the
> SCF iterations in SR calculation are not converging where my input file is
>
>
>
> SystemName  SR.Co
> SystemLabel SR.Co
>
> NumberOfAtoms   131
> NumberOfSpecies2
>
> %block ChemicalSpeciesLabel
>   1   6  C
>   2   27 Co
> %endblock ChemicalSpeciesLabel
>
> PAO.BasisSize  SZP
> PAO.EnergyShift  0.05 Ry
> PAO.SplitNorm0.2
&

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

I have never tried, I don't know if there are any restrictions using both
simultaneously. :(

So a careful test of everything to see if it behaves as expected would be
required, I think. ;)

Den tir. 16. jun. 2020 kl. 15.32 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:

> Thank you again Nick! Just a follow up question are we allowed to use
> LDA+U in TranSIESTA + TbTrans?
>
> Is that applicable? Has anyone published or tested such exchange
> correlation for current voltage calculations? Any further comments would be
> highly appreciated!
>
> Thank you and looking forward to your thoughts!
>
> EL-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
>
> *From: *El-abed Haidar 
> *Sent: *Tuesday, 16 June 2020 10:43 PM
> *To: *Nick Papior ; siesta-l 
> *Subject: *RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
>
>
>
> Thank you very much Nick!
>
> No wonder my calculations were taking that much long!
>
> El-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
>
> *From: *Nick Papior 
> *Sent: *Tuesday, 16 June 2020 4:41 PM
> *To: *siesta-l ; El-abed Haidar
> 
> *Subject: *Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
>
>
>
> Hi,
>
>
>
> 1. Original poster. Could you please try read the manual. Your problem are
> multiple, the electronic structure parameters are insufficient and you are
> not using the electrodes as they should. I.e. they are not bulk like.
>
>
>
> Your simulation requires the use of real-space self-energies, see
> https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417
> <https://protect-au.mimecast.com/s/Ty4RC91WPRTZl1JQcoJX1f?domain=journals.aps.org>
>  .
>
> However, if you are a first in doing transiesta/tbtrans calculations you
> should not start with something this complicated... :(
>
>
>
> 2. @El-abed Haidar , a comment on the input
> suggested.
>
>from -999.99893 eV - V/2 to -10. kT - V/2
>
> Don't do this! You should probably never go below -100 eV, the default -40
> eV should be sufficient for most systems, but -1000 eV is definitely too
> much.
>
> Also, "used-atoms 63" should only be supplied in case you have a subset
> electrode calculation. Otherwise remove this line.
>
>
>
> / Nick
>
>
>
> Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar <
> ehai2...@uni.sydney.edu.au>:
>
> Hi Rayan
>
> Quick question what is the transport direction?
>
> I feel there are some essential blocks missing. Those are generally
> required for a TranSIESTA and TbTrans calculation. Good luck!
>
>
>
> %block TS.ChemPots
>
>   Left
>
>   Right
>
> %endblock TS.ChemPots
>
> %block TS.ChemPot.Left
>
>   mu V/2
>
>   contour.eq
>
> begin
>
>   c-Left
>
>   t-Left
>
> end
>
> %endblock TS.ChemPot.Left
>
> %block TS.ChemPot.Right
>
>   mu -V/2
>
>   contour.eq
>
> begin
>
>   c-Right
>
>   t-Right
>
> end
>
> %endblock TS.ChemPot.Right
>
> TS.Elecs.Bulk true
>
> TS.Elecs.DM.Update cross-terms
>
> TS.Elecs.GF.ReUse true
>
> %block TS.Elecs
>
>   Left
>
>   Right
>
> %endblock TS.Elecs
>
> %block TS.Elec.Left
>
>   HS ./left.TSHS
>
>   chem-pot Left
>
>   semi-inf-dir -a2
>
>   elec-pos begin 1
>
>   used-atoms 63
>
> %endblock TS.Elec.Left
>
> %block TS.Elec.Right
>
>   HS ./right.TSHS
>
>   chem-pot Right
>
>   semi-inf-dir +a2
>
>   elec-pos end -1
>
>   used-atoms 63
>
> %endblock TS.Elec.Right
>
> TS.Contours.Eq.Pole2.5 eV
>
> %block TS.Contour.c-Left
>
>   part circle
>
>from -999.99893 eV + V/2 to -10. kT + V/2
>
> points 50
>
>  method g-legendre
>
> %endblock TS.Contour.c-Left
>
> %block TS.Contour.t-Left
>
>   part tail
>
>from prev to inf
>
> points 10
>
>  method g-fermi
>
> %endblock TS.Contour.t-Left
>
> %block TS.Contour.c-Right
>
>   part circle
>
>from -999.99893 eV - V/2 to -10. kT - V/2
>
> points 50
>
>  method g-legendre
>
> %endblock TS.Contour.c-Right
>
> %block TS.Contour.t-Right
>
>   part tail
>
>from prev to inf
>
> points 10
>
>  method g-fermi
>
> %endblock TS.Contour.t-Right
>
> TS.Elecs

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[El-abed Haidar]

Thank you again Nick! Just a follow up question are we allowed to use LDA+U in 
TranSIESTA + TbTrans?
Is that applicable? Has anyone published or tested such exchange correlation 
for current voltage calculations? Any further comments would be highly 
appreciated!
Thank you and looking forward to your thoughts!
EL-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au>
Sent: Tuesday, 16 June 2020 10:43 PM
To: Nick Papior<mailto:nickpap...@gmail.com>; siesta-l<mailto:siesta-l@uam.es>
Subject: RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Thank you very much Nick!
No wonder my calculations were taking that much long!
El-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: Nick Papior<mailto:nickpap...@gmail.com>
Sent: Tuesday, 16 June 2020 4:41 PM
To: siesta-l<mailto:siesta-l@uam.es>; El-abed 
Haidar<mailto:ehai2...@uni.sydney.edu.au>
Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Hi,

1. Original poster. Could you please try read the manual. Your problem are 
multiple, the electronic structure parameters are insufficient and you are not 
using the electrodes as they should. I.e. they are not bulk like.

Your simulation requires the use of real-space self-energies, see 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417<https://protect-au.mimecast.com/s/Ty4RC91WPRTZl1JQcoJX1f?domain=journals.aps.org>
 .
However, if you are a first in doing transiesta/tbtrans calculations you should 
not start with something this complicated... :(

2. @El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au>, a comment on the input 
suggested.
   from -999.99893 eV - V/2 to -10. kT - V/2
Don't do this! You should probably never go below -100 eV, the default -40 eV 
should be sufficient for most systems, but -1000 eV is definitely too much.
Also, "used-atoms 63" should only be supplied in case you have a subset 
electrode calculation. Otherwise remove this line.

/ Nick

Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar 
mailto:ehai2...@uni.sydney.edu.au>>:
Hi Rayan
Quick question what is the transport direction?
I feel there are some essential blocks missing. Those are generally required 
for a TranSIESTA and TbTrans calculation. Good luck!

%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
  mu V/2
  contour.eq
begin
  c-Left
  t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
begin
  c-Right
  t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ./left.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
  used-atoms 63
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ./right.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
  used-atoms 63
%endblock TS.Elec.Right
TS.Contours.Eq.Pole2.5 eV
%block TS.Contour.c-Left
  part circle
   from -999.99893 eV + V/2 to -10. kT + V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from -999.99893 eV - V/2 to -10. kT - V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta0.000100 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
 method mid-rule
%endblock TS.Contour.nEq.neq
# TBtrans options
TBT.T.Eig 5
TBT.Elecs.Eta0.136058 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from   -2.0 eV to2.0 eV
delta0.00800 eV
 method mid-rule
%endblock TBT.Contour.neq

TBT.DOS.A.All  true
TBT.CDF.MPI true
TS.Voltage 0.0 eV


El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder<mailto:rayanroro321...@gmail.com>
Sent: Monday, 15 June 2020 6:04 AM
To: siesta-l@uam.es<mailto:siesta-l@uam.es>
Subject: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Dear all,

I am a phd student and I am new to siesta , I am doing a Transiesta calculation 
for a system that consist of two graphene sheets sandwiching three cobalt 
atoms, as the electrode calculation is successfully done, the SCF iterations in 
SR calculation are not converging where my input

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[El-abed Haidar]

What should I be looking for? Because as far I have been aware of it has been 
highly recommended to utilize both simultaneously.
My question in other words: What should I test exactly? U and J did you mean?
Thank you and really appreciate your time!
EL-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: Nick Papior<mailto:nickpap...@gmail.com>
Sent: Tuesday, 16 June 2020 11:35 PM
To: El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au>
Cc: siesta-l<mailto:siesta-l@uam.es>
Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

I have never tried, I don't know if there are any restrictions using both 
simultaneously. :(

So a careful test of everything to see if it behaves as expected would be 
required, I think. ;)

Den tir. 16. jun. 2020 kl. 15.32 skrev El-abed Haidar 
mailto:ehai2...@uni.sydney.edu.au>>:
Thank you again Nick! Just a follow up question are we allowed to use LDA+U in 
TranSIESTA + TbTrans?
Is that applicable? Has anyone published or tested such exchange correlation 
for current voltage calculations? Any further comments would be highly 
appreciated!
Thank you and looking forward to your thoughts!
EL-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au>
Sent: Tuesday, 16 June 2020 10:43 PM
To: Nick Papior<mailto:nickpap...@gmail.com>; siesta-l<mailto:siesta-l@uam.es>
Subject: RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Thank you very much Nick!
No wonder my calculations were taking that much long!
El-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: Nick Papior<mailto:nickpap...@gmail.com>
Sent: Tuesday, 16 June 2020 4:41 PM
To: siesta-l<mailto:siesta-l@uam.es>; El-abed 
Haidar<mailto:ehai2...@uni.sydney.edu.au>
Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Hi,

1. Original poster. Could you please try read the manual. Your problem are 
multiple, the electronic structure parameters are insufficient and you are not 
using the electrodes as they should. I.e. they are not bulk like.

Your simulation requires the use of real-space self-energies, see 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417<https://protect-au.mimecast.com/s/6sxiCJyBrGf4jNBZCVeMd9?domain=journals.aps.org>
 .
However, if you are a first in doing transiesta/tbtrans calculations you should 
not start with something this complicated... :(

2. @El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au>, a comment on the input 
suggested.
   from -999.99893 eV - V/2 to -10. kT - V/2
Don't do this! You should probably never go below -100 eV, the default -40 eV 
should be sufficient for most systems, but -1000 eV is definitely too much.
Also, "used-atoms 63" should only be supplied in case you have a subset 
electrode calculation. Otherwise remove this line.

/ Nick

Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar 
mailto:ehai2...@uni.sydney.edu.au>>:
Hi Rayan
Quick question what is the transport direction?
I feel there are some essential blocks missing. Those are generally required 
for a TranSIESTA and TbTrans calculation. Good luck!

%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
  mu V/2
  contour.eq
begin
  c-Left
  t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
begin
  c-Right
  t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ./left.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
  used-atoms 63
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ./right.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
  used-atoms 63
%endblock TS.Elec.Right
TS.Contours.Eq.Pole2.5 eV
%block TS.Contour.c-Left
  part circle
   from -999.99893 eV + V/2 to -10. kT + V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from -999.99893 eV - V/2 to -10. kT - V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta0.000100 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
 method mid-rule
%endblock TS.Contour.nEq.neq
# TBtrans 

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[El-abed Haidar]

Hi Rayan
Quick question what is the transport direction?
I feel there are some essential blocks missing. Those are generally required 
for a TranSIESTA and TbTrans calculation. Good luck!

%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
  mu V/2
  contour.eq
begin
  c-Left
  t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
begin
  c-Right
  t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ./left.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
  used-atoms 63
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ./right.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
  used-atoms 63
%endblock TS.Elec.Right
TS.Contours.Eq.Pole2.5 eV
%block TS.Contour.c-Left
  part circle
   from -999.99893 eV + V/2 to -10. kT + V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from -999.99893 eV - V/2 to -10. kT - V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta0.000100 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
 method mid-rule
%endblock TS.Contour.nEq.neq
# TBtrans options
TBT.T.Eig 5
TBT.Elecs.Eta0.136058 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from   -2.0 eV to2.0 eV
delta0.00800 eV
 method mid-rule
%endblock TBT.Contour.neq

TBT.DOS.A.All  true
TBT.CDF.MPI true
TS.Voltage 0.0 eV


El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder<mailto:rayanroro321...@gmail.com>
Sent: Monday, 15 June 2020 6:04 AM
To: siesta-l@uam.es<mailto:siesta-l@uam.es>
Subject: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Dear all,

I am a phd student and I am new to siesta , I am doing a Transiesta calculation 
for a system that consist of two graphene sheets sandwiching three cobalt 
atoms, as the electrode calculation is successfully done, the SCF iterations in 
SR calculation are not converging where my input file is

SystemName  SR.Co
SystemLabel SR.Co

NumberOfAtoms   131
NumberOfSpecies2

%block ChemicalSpeciesLabel
  1   6  C
  2   27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize  SZP
PAO.EnergyShift  0.05 Ry
PAO.SplitNorm0.2

==
==
# K-points

%block kgrid_Monkhorst_Pack
   1   0   0  0.0
   0   1   0  0.0
   0   0   1  0.5
%endblock Kgrid_Monkhorst_Pack
==
==
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL
LatticeConstant 1.00 Ang

%block LatticeVectors
17.016 0.000 0.000
0.000 9.824 0.000
0.000 0. 14.000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies

0.000 0.000 0.000 1
1.418 0.000 0.000 1
2.127 1.228 0.000 1
3.545 1.228 0.000 1
4.254 0.000 0.000 1
5.672 0.000 0.000 1
6.381  1.228 0.000 1
7.799  1.228 0.000 1
8.508  0.000 0.000 1
9.926  0.000 0.000 1
10.635 1.228 0.000 1
12.053 1.228 0.000 1
12.762 0.000 0.000 1
14.180 0.000 0.000 1
14.889 1.228 0.000 1
16.304 1.228 0.000 1
0.000  2.456 0.000 1
1.418  2.456 0.000 1
2.127  3.684 0.000 1
3.545  3.684 0.000 1
4.254  2.456 0.000 1
5.672  2.456 0.000 1
6.381  3.684 0.000 1
7.799  3.684 0.000 1
8.508  2.456 0.000 1
9.926  2.456 0.000 1
10.635 3.684 0.000 1
12.053 3.684 0.000 1
12.762 2.456 0.000 1
14.180 2.456 0.000 1
14.889 3.684 0.000 1
16.307 3.684 0.000 1
0.000  4.912 0.000 1
1.418  4.912 0.000 1
2.127  6.140 0.000 1
3.545  6.140 0.000 1
4.254  4.912 0.000 1
5.672  4.912 0.000 1
6.381  6.140 0.000 1
7.799  6.140 0.000 1
8.508  4.912 0.000 1
9.926  4.912 0.000 1
10.635 6.140 0.000 1
12.053 6.140 0.000 1
12.762 4.912 0.000 1
14.180 4.912 0.000 1
14.889 6.140 0.000 1
16.307 6.140 0.000 1
0.000  7.368 0.000 1
1.418  7.368 0.000 1
2.127  8.596 0.000 1
3.545  8.596 0.000 1
4.254  7.368 0.000 1
5.672  7.368 0.000 1
6.381  8.596 0.000 1
7.799  8.596 0.000 1
8.508  7.368 0.000 1
9.926  7.368 0.000 1
10.635 8.596 0.000 1
12.053 8.596 0.000 1
12.762 7.368 0.000 1
14.180 7.368 0.000 1
14.889 8.596 0.000 1
16.307 8.596 0.000 1
7.0900  4.912 1.400 2
7.0900  4.912 3.900 2
7.0900  4.912 6.400 2
0.000  0.000 7.800 1
1.418  0.000 7.800 1
2.127 1.228 7.800 1
3.545 1.228 7.800 1
4.254 0.000 7.800 1
5.672

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[rayan moukhadder]

Dear all,

I am a phd student and I am new to siesta , I am doing a Transiesta
calculation for a system that consist of two graphene sheets sandwiching
three cobalt atoms, as the electrode calculation is successfully done, the
SCF iterations in SR calculation are not converging where my input file is

SystemName  SR.Co
SystemLabel SR.Co

NumberOfAtoms   131
NumberOfSpecies2

%block ChemicalSpeciesLabel
  1   6  C
  2   27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize  SZP
PAO.EnergyShift  0.05 Ry
PAO.SplitNorm0.2

==
==
# K-points

%block kgrid_Monkhorst_Pack
   1   0   0  0.0
   0   1   0  0.0
   0   0   1  0.5
%endblock Kgrid_Monkhorst_Pack
==
==
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL
LatticeConstant 1.00 Ang

%block LatticeVectors
17.016 0.000 0.000
0.000 9.824 0.000
0.000 0. 14.000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies

0.000 0.000 0.000 1
1.418 0.000 0.000 1
2.127 1.228 0.000 1
3.545 1.228 0.000 1
4.254 0.000 0.000 1
5.672 0.000 0.000 1
6.381  1.228 0.000 1
7.799  1.228 0.000 1
8.508  0.000 0.000 1
9.926  0.000 0.000 1
10.635 1.228 0.000 1
12.053 1.228 0.000 1
12.762 0.000 0.000 1
14.180 0.000 0.000 1
14.889 1.228 0.000 1
16.304 1.228 0.000 1
0.000  2.456 0.000 1
1.418  2.456 0.000 1
2.127  3.684 0.000 1
3.545  3.684 0.000 1
4.254  2.456 0.000 1
5.672  2.456 0.000 1
6.381  3.684 0.000 1
7.799  3.684 0.000 1
8.508  2.456 0.000 1
9.926  2.456 0.000 1
10.635 3.684 0.000 1
12.053 3.684 0.000 1
12.762 2.456 0.000 1
14.180 2.456 0.000 1
14.889 3.684 0.000 1
16.307 3.684 0.000 1
0.000  4.912 0.000 1
1.418  4.912 0.000 1
2.127  6.140 0.000 1
3.545  6.140 0.000 1
4.254  4.912 0.000 1
5.672  4.912 0.000 1
6.381  6.140 0.000 1
7.799  6.140 0.000 1
8.508  4.912 0.000 1
9.926  4.912 0.000 1
10.635 6.140 0.000 1
12.053 6.140 0.000 1
12.762 4.912 0.000 1
14.180 4.912 0.000 1
14.889 6.140 0.000 1
16.307 6.140 0.000 1
0.000  7.368 0.000 1
1.418  7.368 0.000 1
2.127  8.596 0.000 1
3.545  8.596 0.000 1
4.254  7.368 0.000 1
5.672  7.368 0.000 1
6.381  8.596 0.000 1
7.799  8.596 0.000 1
8.508  7.368 0.000 1
9.926  7.368 0.000 1
10.635 8.596 0.000 1
12.053 8.596 0.000 1
12.762 7.368 0.000 1
14.180 7.368 0.000 1
14.889 8.596 0.000 1
16.307 8.596 0.000 1
7.0900  4.912 1.400 2
7.0900  4.912 3.900 2
7.0900  4.912 6.400 2
0.000  0.000 7.800 1
1.418  0.000 7.800 1
2.127 1.228 7.800 1
3.545 1.228 7.800 1
4.254 0.000 7.800 1
5.672 0.000 7.800 1
6.381  1.228 7.800 1
7.799  1.228 7.800 1
8.508  0.000 7.800 1
9.926  0.000 7.800 1
10.635 1.228 7.800 1
12.053 1.228 7.800 1
12.762 0.000 7.800 1
14.180 0.000 7.800 1
14.889 1.228 7.800 1
16.304 1.228 7.800 1
0.000  2.456 7.800 1
1.418  2.456 7.800 1
2.127  3.684 7.800 1
3.545  3.684 7.800 1
4.254  2.456 7.800 1
5.672  2.456 7.800 1
6.381  3.684 7.800 1
7.799  3.684 7.800 1
8.508  2.456 7.800 1
9.926  2.456 7.800 1
10.635 3.684 7.800 1
12.053 3.684 7.800 1
12.762 2.456 7.800 1
14.180 2.456 7.800 1
14.889 3.684 7.800 1
16.307 3.684 7.800 1
0.000  4.912 7.800 1
1.418  4.912 7.800 1
2.127  6.140 7.800 1
3.545  6.140 7.800 1
4.254  4.912 7.800 1
5.672  4.912 7.800 1
6.381  6.140 7.800 1
7.799  6.140 7.800 1
8.508  4.912 7.800 1
9.926  4.912 7.800 1
10.635 6.140 7.800 1
12.053 6.140 7.800 1
12.762 4.912 7.800 1
14.180 4.912 7.800 1
14.889 6.140 7.800 1
16.307 6.140 7.800 1
0.000  7.368 7.800 1
1.418  7.368 7.800 1
2.127  8.596 7.800 1
3.545  8.596 7.800 1
4.254  7.368 7.800 1
5.672  7.368 7.800 1
6.381  8.596 7.800 1
7.799  8.596 7.800 1
8.508  7.368 7.800 1
9.926  7.368 7.800 1
10.635 8.596 7.800 1
12.053 8.596 7.800 1
12.762 7.368 7.800 1
14.180 7.368 7.800 1
14.889 8.596 7.800 1
16.307 8.596 7.800 1

%endblock AtomicCoordinatesAndAtomicSpecies

# General variables

ElectronicTemperature  100 K
MeshCutoff   350. Ry
xc.functional GGA   # Exchange-correlation functional
xc.authorsPBE
SpinPolarized .false.
SolutionMethod Transiesta

==
==
# SCF variables

DM.MixSCF1   T
MaxSCFIterations4000   # Maximum number of SCF iter
DM.MixingWeight   0.2  # New DM amount for next SCF cycle
DM.Tolerance  0.0009# Tolerance in maximum difference
DM.UseSaveDM  true  # to use continuation files
DM.NumberPulay 5
Diag.DivideAndConquer  no
Diag.ParallelOverK yes

==
==
# MD variables

MD.FinalTimeStep 1
MD.TypeOfRun CG
MD.NumCGsteps 000
MD.UseSaveXV  .true.

==
==
# Output variables

WriteMullikenPop1
WriteBands  

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Adeel ahmed awan]

Dear siesta users,
 I am new to siesta. Can any one help me how to find the magnetic moment of
any compound. In my case i have SrTiO3( Strontium Titanate) .

thanks in advance.

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Batoul Jomaa]

 Dear all

I'm trying to generate pseudopotential but i have this problem how can i
fix it ?


../../Utils/pg.sh Si.tm2.inp
../../Utils/pg.sh: 45: ../../Utils/pg.sh:
/home/SIESTA-4.0.2/siesta-4.0.2/Pseudo/atom-4.2.7-100/Tutori
al/Utils/../../atm:
not found
cp: cannot stat 'VPSOUT': No such file or directory
cp: cannot stat 'VPSFMT': No such file or directory

Thank you,

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

If you have specific questions regarding sisl, then please direct them to
this page:
https://github.com/zerothi/sisl

However, it probably means that you haven't calculated the DOS from the
green function.

2018-04-01 7:01 GMT+02:00 maryam jamaati :

> Dear siesta users,
>
> When we run the command sdata trans.TBT.nc—atom 181-197 —dos —out dos.dat
> in vrsion 4.1.b3 of tbttrans, we recieve below error:
>
> Traceback (most recent call last):
> File "/home/sf/.local/bin/sdata", line 11, in 
> sys.exit(sdata())
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/sdata.py",
> line 123, in sdata
> p.parse_args(argv, namespace=ns)
> File "/usr/lib/python2.7/argparse.py", line 1690, in parse_args
> args, argv = self.parse_known_args(args, namespace)
> File "/usr/lib/python2.7/argparse.py", line 1722, in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> File "/usr/lib/python2.7/argparse.py", line 1928, in _parse_known_args
> start_index = consume_optional(start_index)
> File "/usr/lib/python2.7/argparse.py", line 1868, in consume_optional
> take_action(action, args, option_string)
> File "/usr/lib/python2.7/argparse.py", line 1796, in take_action
> action(self, namespace, argument_values, option_string)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/cmd.py",
> line 217, in run
> A(*Aargs, **Akwargs)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/cmd.py",
> line 184, in collect
> return func(self, *args, **kwargs)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
> line 1578, in assign_E
> return func(self, *args, **kwargs)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
> line 1810, in *call*
> data = ns._tbt.DOS(kavg=ns._krng, orbital=ns._Orng, norm=ns._norm)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
> line 723, in DOS
> return self._DOS(self._value_E('DOS', kavg=kavg, E=E),
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
> line 149, in _value_E
> return self._value_avg(name, tree, kavg)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
> line 112, in _value_avg
> v = self._variable(name, tree=tree)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/sile.py", line
> 753, in _variable
> return self._variables(self, name, tree=tree)
> File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/sile.py", line
> 766, in _variables
> return n.variables[name]
> KeyError: 'DOS'
>
> We would be pleased if one could help us to solve the problem.
>
> Sincerely yours,
> maryam jamaati
>



-- 
Kind regards Nick

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[maryam jamaati]

Dear siesta users,

When we run the command sdata trans.TBT.nc—atom 181-197 —dos —out dos.dat
in vrsion 4.1.b3 of tbttrans, we recieve below error:

Traceback (most recent call last):
File "/home/sf/.local/bin/sdata", line 11, in 
sys.exit(sdata())
File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/sdata.py",
line 123, in sdata
p.parse_args(argv, namespace=ns)
File "/usr/lib/python2.7/argparse.py", line 1690, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1722, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1928, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python2.7/argparse.py", line 1868, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python2.7/argparse.py", line 1796, in take_action
action(self, namespace, argument_values, option_string)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/cmd.py", line
217, in run
A(*Aargs, **Akwargs)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/cmd.py", line
184, in collect
return func(self, *args, **kwargs)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 1578, in assign_E
return func(self, *args, **kwargs)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 1810, in *call*
data = ns._tbt.DOS(kavg=ns._krng, orbital=ns._Orng, norm=ns._norm)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 723, in DOS
return self._DOS(self._value_E('DOS', kavg=kavg, E=E),
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 149, in _value_E
return self._value_avg(name, tree, kavg)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 112, in _value_avg
v = self._variable(name, tree=tree)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/sile.py", line
753, in _variable
return self._variables(self, name, tree=tree)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/sile.py", line
766, in _variables
return n.variables[name]
KeyError: 'DOS'

We would be pleased if one could help us to solve the problem.

Sincerely yours,
maryam jamaati

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[masoudeh maleki]

Dear sir,

I'm using siesta code to investigate the effect of doping on bandstructure
and PDOS of the crystal of tin oxide with tetragonal unitcell. I made a
2*2*2 supercell of it, and replaced one O atom with my dopant.
1. After doping should I find optimized lattice constant or optimized
lattice constant of pure structure is acceptable?
2. after doping how can I measure the increasment or decreasment of the
structure volume?
2. I plot diagram of Pdos of pure tinoxide with 48 atoms, and I want to
shift top of the valance band to zero. But the quantity of energy read from
the filename.eig file (5.0578) is different from the value in the diagram
of pdos( about 0.6). Why?
2. For shifting the diagram of doped tinoxide, howmuch Should I shift it?
As much as pure tinoxide read from the filename.eig or from the
filename.eig of doped tinoxide?

Yours sincerely

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Harsh Shah]

Dear Siesta user,

I am really new to this siesta software & I am just getting started with it.

I had a few basic questions:
1.Which is the best software to use with   siesta for making structures?
2.How can we define whether the   structure is periodic or not and
where
 to define it?
3.How to optimize a structure?

I would really appreciate if you could help me out.

With Best Wishes,
Harsh

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Farzaneh Farzadi]

*Thanks a lot* !

On Tue, Oct 24, 2017 at 6:05 PM, Mostafa Shabani <
mostafa.nanophys...@gmail.com> wrote:

> The easy way to do that to update your old fdf file to the new one you can
> use ts2ts in ( Util/TS/ts2ts)
>
> On Oct 24, 2017 12:22, "Mostafa Shabani" 
> wrote:
>
>> You should change the input fdf parameters based on new version.
>>
>> On Oct 23, 2017 18:00, "Farzaneh Farzadi"  wrote:
>>
>>> *Dear users *
>>>
>>> I
>>> * have installed  Tbtrans in 4.1-b3 version recently. before that, i
>>> used 3.2 version.*
>>> *now when i run my fdf file in new version, i run into an
>>> error,however,  it is successfully performed *
>>>
>>> *in 3.2 version.*
>>> *error is:*
>>> reinit: 
>>> ---
>>> reinit: System Name: stagg
>>> reinit: 
>>> ---
>>> reinit: System Label: stagger-scat
>>> reinit: 
>>> ---
>>> Could not find electrode: left
>>> Could not find electrode: left
>>> Stopping Program from Node:0
>>> Stopping Program from Node:0
>>> 
>>> --
>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> *my some part of input is as follows:*
>>>
>>> #==
>>> #   *** GENGF OPTIONS ***
>>> #==
>>>
>>> TS.ComplexContour.Emin-24 eV
>>> TS.ComplexContour.NPoles   10
>>> TS.ComplexContour.NCircle  26
>>> TS.ComplexContour.NLine11
>>>
>>> # BIAS OPTIONS
>>>
>>> TS.biasContour.NumPoints   10
>>>
>>> # TS OPTIONS
>>>
>>> TS.Voltage 0.3  eV
>>>
>>> # TBT OPTIONS
>>> TS.TBT.Emin -3 eV
>>> TS.TBT.Emax +3 eV
>>> TS.TBT.NPoints 500
>>> TS.TBT.NEigen 3
>>> TS.TBT.Eta0.01 Ry
>>> # Write electrode hamiltonian
>>> TS.SaveHS   .true.
>>> TS.SaveLead .true.
>>>
>>> WriteDM T
>>> TS.MixH T
>>> TS.UpdateDMCROnly   T
>>> SCFMustConverge T
>>> #==
>>> #*** ELECTRODE 
>>> #==
>>>
>>>
>>> #LEFT ELECTRODE
>>> TS.HSFileLeft  ./stagg-elec.TSHS
>>> TS.NumUsedAtomsLeft   27
>>> TS.BufferAtomsLeft0
>>>
>>> #RIGHT ELECTRODE
>>> TS.HSFileRight  ./stagg-elec.TSHS
>>> TS.NumUsedAtomsRight  27
>>> TS.BufferAtomsRight   0
>>>
>>> #==
>>> #*** SCATTER 
>>> #==
>>>
>>> TS.TBT.HSFile   ./stagger-scat.TSHS
>>>
>>> *what changes should be done to remove the error?*
>>> *Thanks a lot*
>>>
>>

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Mostafa Shabani]

The easy way to do that to update your old fdf file to the new one you can
use ts2ts in ( Util/TS/ts2ts)

On Oct 24, 2017 12:22, "Mostafa Shabani" 
wrote:

> You should change the input fdf parameters based on new version.
>
> On Oct 23, 2017 18:00, "Farzaneh Farzadi"  wrote:
>
>> *Dear users *
>>
>> I
>> * have installed  Tbtrans in 4.1-b3 version recently. before that, i used
>> 3.2 version.*
>> *now when i run my fdf file in new version, i run into an error,however,
>> it is successfully performed *
>>
>> *in 3.2 version.*
>> *error is:*
>> reinit: 
>> ---
>> reinit: System Name: stagg
>> reinit: 
>> ---
>> reinit: System Label: stagger-scat
>> reinit: 
>> ---
>> Could not find electrode: left
>> Could not find electrode: left
>> Stopping Program from Node:0
>> Stopping Program from Node:0
>> 
>> --
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> *my some part of input is as follows:*
>>
>> #==
>> #   *** GENGF OPTIONS ***
>> #==
>>
>> TS.ComplexContour.Emin-24 eV
>> TS.ComplexContour.NPoles   10
>> TS.ComplexContour.NCircle  26
>> TS.ComplexContour.NLine11
>>
>> # BIAS OPTIONS
>>
>> TS.biasContour.NumPoints   10
>>
>> # TS OPTIONS
>>
>> TS.Voltage 0.3  eV
>>
>> # TBT OPTIONS
>> TS.TBT.Emin -3 eV
>> TS.TBT.Emax +3 eV
>> TS.TBT.NPoints 500
>> TS.TBT.NEigen 3
>> TS.TBT.Eta0.01 Ry
>> # Write electrode hamiltonian
>> TS.SaveHS   .true.
>> TS.SaveLead .true.
>>
>> WriteDM T
>> TS.MixH T
>> TS.UpdateDMCROnly   T
>> SCFMustConverge T
>> #==
>> #*** ELECTRODE 
>> #==
>>
>>
>> #LEFT ELECTRODE
>> TS.HSFileLeft  ./stagg-elec.TSHS
>> TS.NumUsedAtomsLeft   27
>> TS.BufferAtomsLeft0
>>
>> #RIGHT ELECTRODE
>> TS.HSFileRight  ./stagg-elec.TSHS
>> TS.NumUsedAtomsRight  27
>> TS.BufferAtomsRight   0
>>
>> #==
>> #*** SCATTER 
>> #==
>>
>> TS.TBT.HSFile   ./stagger-scat.TSHS
>>
>> *what changes should be done to remove the error?*
>> *Thanks a lot*
>>
>

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Mostafa Shabani]

You should change the input fdf parameters based on new version.

On Oct 23, 2017 18:00, "Farzaneh Farzadi"  wrote:

> *Dear users *
>
> I
> * have installed  Tbtrans in 4.1-b3 version recently. before that, i used
> 3.2 version.*
> *now when i run my fdf file in new version, i run into an error,however,
> it is successfully performed *
>
> *in 3.2 version.*
> *error is:*
> reinit: 
> ---
> reinit: System Name: stagg
> reinit: 
> ---
> reinit: System Label: stagger-scat
> reinit: 
> ---
> Could not find electrode: left
> Could not find electrode: left
> Stopping Program from Node:0
> Stopping Program from Node:0
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> *my some part of input is as follows:*
>
> #==
> #   *** GENGF OPTIONS ***
> #==
>
> TS.ComplexContour.Emin-24 eV
> TS.ComplexContour.NPoles   10
> TS.ComplexContour.NCircle  26
> TS.ComplexContour.NLine11
>
> # BIAS OPTIONS
>
> TS.biasContour.NumPoints   10
>
> # TS OPTIONS
>
> TS.Voltage 0.3  eV
>
> # TBT OPTIONS
> TS.TBT.Emin -3 eV
> TS.TBT.Emax +3 eV
> TS.TBT.NPoints 500
> TS.TBT.NEigen 3
> TS.TBT.Eta0.01 Ry
> # Write electrode hamiltonian
> TS.SaveHS   .true.
> TS.SaveLead .true.
>
> WriteDM T
> TS.MixH T
> TS.UpdateDMCROnly   T
> SCFMustConverge T
> #==
> #*** ELECTRODE 
> #==
>
>
> #LEFT ELECTRODE
> TS.HSFileLeft  ./stagg-elec.TSHS
> TS.NumUsedAtomsLeft   27
> TS.BufferAtomsLeft0
>
> #RIGHT ELECTRODE
> TS.HSFileRight  ./stagg-elec.TSHS
> TS.NumUsedAtomsRight  27
> TS.BufferAtomsRight   0
>
> #==
> #*** SCATTER 
> #==
>
> TS.TBT.HSFile   ./stagger-scat.TSHS
>
> *what changes should be done to remove the error?*
> *Thanks a lot*
>

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

Please read the changes that were made in 4.1 (basically everything
regarding transiesta/tbtrans has changed).

See here
https://launchpad.net/siesta/4.1

Also, please read the new manual for siesta(transiesta) and the new
separate tbtrans manual.

2017-10-23 9:11 GMT+02:00 Farzaneh Farzadi :

> *Dear users *
>
> I
> * have installed  Tbtrans in 4.1-b3 version recently. before that, i used
> 3.2 version.*
> *now when i run my fdf file in new version, i run into an error,however,
> it is successfully performed *
>
> *in 3.2 version.*
> *error is:*
> reinit: 
> ---
> reinit: System Name: stagg
> reinit: 
> ---
> reinit: System Label: stagger-scat
> reinit: 
> ---
> Could not find electrode: left
> Could not find electrode: left
> Stopping Program from Node:0
> Stopping Program from Node:0
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> *my some part of input is as follows:*
>
> #==
> #   *** GENGF OPTIONS ***
> #==
>
> TS.ComplexContour.Emin-24 eV
> TS.ComplexContour.NPoles   10
> TS.ComplexContour.NCircle  26
> TS.ComplexContour.NLine11
>
> # BIAS OPTIONS
>
> TS.biasContour.NumPoints   10
>
> # TS OPTIONS
>
> TS.Voltage 0.3  eV
>
> # TBT OPTIONS
> TS.TBT.Emin -3 eV
> TS.TBT.Emax +3 eV
> TS.TBT.NPoints 500
> TS.TBT.NEigen 3
> TS.TBT.Eta0.01 Ry
> # Write electrode hamiltonian
> TS.SaveHS   .true.
> TS.SaveLead .true.
>
> WriteDM T
> TS.MixH T
> TS.UpdateDMCROnly   T
> SCFMustConverge T
> #==
> #*** ELECTRODE 
> #==
>
>
> #LEFT ELECTRODE
> TS.HSFileLeft  ./stagg-elec.TSHS
> TS.NumUsedAtomsLeft   27
> TS.BufferAtomsLeft0
>
> #RIGHT ELECTRODE
> TS.HSFileRight  ./stagg-elec.TSHS
> TS.NumUsedAtomsRight  27
> TS.BufferAtomsRight   0
>
> #==
> #*** SCATTER 
> #==
>
> TS.TBT.HSFile   ./stagger-scat.TSHS
>
> *what changes should be done to remove the error?*
> *Thanks a lot*
>



-- 
Kind regards Nick

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Farzaneh Farzadi]

*Dear users *

I
* have installed  Tbtrans in 4.1-b3 version recently. before that, i used
3.2 version.*
*now when i run my fdf file in new version, i run into an error,however,
it is successfully performed *

*in 3.2 version.*
*error is:*
reinit:
---
reinit: System Name: stagg
reinit:
---
reinit: System Label: stagger-scat
reinit:
---
Could not find electrode: left
Could not find electrode: left
Stopping Program from Node:0
Stopping Program from Node:0
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

*my some part of input is as follows:*

#==
#   *** GENGF OPTIONS ***
#==

TS.ComplexContour.Emin-24 eV
TS.ComplexContour.NPoles   10
TS.ComplexContour.NCircle  26
TS.ComplexContour.NLine11

# BIAS OPTIONS

TS.biasContour.NumPoints   10

# TS OPTIONS

TS.Voltage 0.3  eV

# TBT OPTIONS
TS.TBT.Emin -3 eV
TS.TBT.Emax +3 eV
TS.TBT.NPoints 500
TS.TBT.NEigen 3
TS.TBT.Eta0.01 Ry
# Write electrode hamiltonian
TS.SaveHS   .true.
TS.SaveLead .true.

WriteDM T
TS.MixH T
TS.UpdateDMCROnly   T
SCFMustConverge T
#==
#*** ELECTRODE 
#==


#LEFT ELECTRODE
TS.HSFileLeft  ./stagg-elec.TSHS
TS.NumUsedAtomsLeft   27
TS.BufferAtomsLeft0

#RIGHT ELECTRODE
TS.HSFileRight  ./stagg-elec.TSHS
TS.NumUsedAtomsRight  27
TS.BufferAtomsRight   0

#==
#*** SCATTER 
#==

TS.TBT.HSFile   ./stagger-scat.TSHS

*what changes should be done to remove the error?*
*Thanks a lot*

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[RCP]

Hi,

Look for line 23 in the source of siesta.F, the traceback says
the problem starts there. You'll get an idea of what the program
was doing.

"Segmentation fault" is too generic an error to say anything precise,
wrong data or-what-not might be a possible cause.

Regards,

Roberto


On 05/09/2017 03:01 AM, Farzaneh Farzadi wrote:

Dear users

Upon the siesta running, I got the following error:


Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0Â  0x7F3B125C2E08
#1Â  0x7F3B125C1F90
#2Â  0x7F3B11CF449F
#3Â  0x42FD98 in diagg_ at diagg.F:252
#4Â  0x421B76 in diagon_ at diagon.F:262
#5Â  0x4BBA80 in __m_compute_dm_MOD_compute_dm at compute_dm.F:60
#6Â  0x4D063D in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80
#7Â  0x404D09 in siesta at siesta.F:23
#8Â  0x7F3B11CDF82F

what should i do?

any help will be appreciated
best regards
farzadi

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Farzaneh Farzadi]

Dear users

Upon the siesta running, I got the following error:


Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0  0x7F3B125C2E08
#1  0x7F3B125C1F90
#2  0x7F3B11CF449F
#3  0x42FD98 in diagg_ at diagg.F:252
#4  0x421B76 in diagon_ at diagon.F:262
#5  0x4BBA80 in __m_compute_dm_MOD_compute_dm at compute_dm.F:60
#6  0x4D063D in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80
#7  0x404D09 in siesta at siesta.F:23
#8  0x7F3B11CDF82F

what should i do?

any help will be appreciated
best regards
farzadi

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Farzaneh Farzadi]

Dear all

I am getting this error while running the transiesta code.
I do not know what the error means.
any help will be really appreciated.


sincerely
Farzadi

.
.
siesta:  384  -107619.3010  -107619.3010  -107619.3010  0.0004 -3.4348
siesta:  385  -107619.3011  -107619.3011  -107619.3011  0.0004 -3.4348
siesta:  386  -107619.3012  -107619.3011  -107619.3011  0.0003 -3.4347

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0  0x7FD48F550E08
#1  0x7FD48F54FF90
#2  0x7FD48EC824AF
#3  0x43152C in diagk_ at diagk.F:364
#4  0x421CF4 in diagon_ at diagon.F:305
#5  0x4BCD85 in __m_compute_dm_MOD_compute_dm at compute_dm.F:60
#6  0x4D2C81 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:94
#7  0x404ED9 in siesta at siesta.F:23
#8  0x7FD48EC6D82F
--
mpirun noticed that process rank 0 with PID 2582 on node linuxfarzadi
exited on signal 11 (Segmentation fault).

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Farzaneh Farzadi]

Dear all

I am getting this error while running the transiesta code.
I do not know what the error means.
any help will be really appreciated.


sincerely
Farzadi

.
.
siesta:  384  -107619.3010  -107619.3010  -107619.3010  0.0004 -3.4348
siesta:  385  -107619.3011  -107619.3011  -107619.3011  0.0004 -3.4348
siesta:  386  -107619.3012  -107619.3011  -107619.3011  0.0003 -3.4347

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0  0x7FD48F550E08
#1  0x7FD48F54FF90
#2  0x7FD48EC824AF
#3  0x43152C in diagk_ at diagk.F:364
#4  0x421CF4 in diagon_ at diagon.F:305
#5  0x4BCD85 in __m_compute_dm_MOD_compute_dm at compute_dm.F:60
#6  0x4D2C81 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:94
#7  0x404ED9 in siesta at siesta.F:23
#8  0x7FD48EC6D82F
--
mpirun noticed that process rank 0 with PID 2582 on node linuxfarzadi
exited on signal 11 (Segmentation fault).

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Ross Brown]

N.B. the siesta list moderator:

Please do not post further correspondence in this thread. Fast has its 
own mailing list referenced below. Thank you.



Hello Soumaia!

As mentioned previously, no help can in general be provided about 
installation. Systems are much too variable. Check the documentation 
provided in the package and consult you local system manager.


BTW, as pointed out in my earlier reply, do NOT use the siesta list 
for queries about fast.



DO use the FAST list. You can subscribe at

http://lists.gforge.inria.fr/mailman/listinfo/nossi-tddft-users

Yours
Ross Brown



On 10/01/17 19:42, Soumaia Djaadi wrote:

Hello Users
I' m trying to install FAST TDDFT code but I have some problams, can you help 
me ?
Djaadi Soumaia.
.
Generators

The following generators are available on this platform:
   Ninja   = Generates build.ninja files (experimental).
   Unix Makefiles  = Generates standard UNIX makefiles.
   CodeBlocks - Unix Makefiles = Generates CodeBlocks project files.
   Eclipse CDT4 - Unix Makefiles
   = Generates Eclipse CDT 4.0 project files.
   KDevelop3   = Generates KDevelop 3 project files.
   KDevelop3 - Unix Makefiles  = Generates KDevelop 3 project files.

[ilaf@localhost build]$ 
-DSIESTA_XC_DIR=/ABSOLUTEPATH/home/siesta-3.2-pl-5/Obj/SiestaXC ../
bash: -DSIESTA_XC_DIR=/ABSOLUTEPATH/home/siesta-3.2-pl-5/Obj/SiestaXC: No such 
file or directory
[ilaf@localhost build]$ -DSIESTA_XC_DIR=/ABSOLUTEPATH//Obj/SiestaXC ../
bash: -DSIESTA_XC_DIR=/ABSOLUTEPATH//Obj/SiestaXC: No such file or directory
[ilaf@localhost build]$
..

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Soumaia Djaadi]

Hello Users 
I' m trying to install FAST TDDFT code but I have some problams, can you help 
me ?
Djaadi Soumaia.
.
Generators

The following generators are available on this platform:
  Ninja   = Generates build.ninja files (experimental).
  Unix Makefiles  = Generates standard UNIX makefiles.
  CodeBlocks - Unix Makefiles = Generates CodeBlocks project files.
  Eclipse CDT4 - Unix Makefiles
  = Generates Eclipse CDT 4.0 project files.
  KDevelop3   = Generates KDevelop 3 project files.
  KDevelop3 - Unix Makefiles  = Generates KDevelop 3 project files.

[ilaf@localhost build]$ 
-DSIESTA_XC_DIR=/ABSOLUTEPATH/home/siesta-3.2-pl-5/Obj/SiestaXC ../
bash: -DSIESTA_XC_DIR=/ABSOLUTEPATH/home/siesta-3.2-pl-5/Obj/SiestaXC: No such 
file or directory
[ilaf@localhost build]$ -DSIESTA_XC_DIR=/ABSOLUTEPATH//Obj/SiestaXC ../
bash: -DSIESTA_XC_DIR=/ABSOLUTEPATH//Obj/SiestaXC: No such file or directory
[ilaf@localhost build]$ 
..

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[asal naz]

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[AAKANKSHA SUD]

Dear Siesta Users
 I am constructing a molecule attached to gold electrode and i am
using siesta 4.1 -b version but on running the scattering run
calculation i get the following error
 Electrode: Left has very few k-points in the semi-infinite direction,
at least 20 is recommended.
Incompatible k-grids...
Electrode file k-grid:
   100   0.
   010   0.
   00   10   0.5000
System k-grid:
   100   0.
   010   0.
   001   0.
Electrode file k-grid should be:
   100   0.
   010   0.
   001   0.
Erroneous electrode setup, check out-put
Stopping Program from Node:0
Could anyone please help
thanking you
aakanksha

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Nick Papior]

You may use sisl which is a command line and python scripting utility. The
command in sisl is `sgeom input.XV -o output.xsf -o output.xyz`.

I also know of Inelastica which should do this with geom2geom command.

2016-11-16 7:17 GMT+01:00 AAKANKSHA SUD :

> dear users
> can anyone please tell me how to convert .xv files or .xsf files into
> .xyz format . is there an utility to do so.please tell if anyone knows
> about it.
> thanks
> aakanksha
>



-- 
Kind regards Nick

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[AAKANKSHA SUD]

dear users
can anyone please tell me how to convert .xv files or .xsf files into
.xyz format . is there an utility to do so.please tell if anyone knows
about it.
thanks
aakanksha