[SIESTA-L] [***Posible SPAM***] Re: Optical Spectrum of Zeolite - not completing

[Krishna Mohan]

Due to some HTML parsing the message is not shown as expected: So I re
entered the message:

Dear List

I am trying to calculate the optical spectrum of a Zeolite compound and we
have its experimental spectrum and
it shows a clear absorption in Visible region (and the pure Zeolite
compound is a colored one).
So we expect that the Siesta’s spectrum would reflect this too.

But when I tried the calculation (Pls see below part for its LOG and Input
file)
it runs and completed SCF cycle and it seems it stuck in the portion:

-
...
130 -0.012952 -0.089863 0.127418
131 0.020422 0.101546 -0.046036
132 0.047941 -0.009764 0.000107
133 -0.043814 -0.020094 -0.131299
134 -0.056622 0.062521 0.031526
135 0.042265 -0.027729 -0.004018
136 -0.016008 0.021773 0.020389
137 0.063636 -0.039750 -0.033829
138 0.055053 0.033202 -0.021522
Tot -0.005242 0.008209 -0.009872
Max 0.337362
Res 0.065680 sqrt( Sum f_i^2 / 3N )
Max 0.337362 constrained

Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 2.89 2.86 1.82 -0.46 -0.58 -0.51
(Free)E + p*V (eV/cell) -19533.6875
Target enthalpy (eV/cell) -19529.8878

coxmol: Writing XMOL coordinates into file zif67optical.xyz

siesta: Program’s energy decomposition (eV):
siesta: Ebs = -5482.245303
siesta: Eions = 23083.627097
siesta: Ena = 3227.550941
siesta: Ekin = 16297.878613
siesta: Enl = -9828.161993
siesta: Eso = 0.00
siesta: Edftu = 0.00
siesta: DEna = -413.734991
siesta: DUscf = 64.552342
siesta: DUext = 0.00
siesta: Exc = -5794.300663
siesta: eta*DQ = 0.00
siesta: Emadel = 0.00
siesta: Emeta = 0.00
siesta: Emolmec = 0.00
siesta: Ekinion = 0.00
siesta: Eharris = -19529.842846
siesta: Etot = -19529.842848
siesta: FreeEng = -19529.887822

siesta: Final energy (eV):
siesta: Band Struct. = -5482.245303
siesta: Kinetic = 16297.878613
siesta: Hartree = 30900.513857
siesta: Edftu = 0.00
siesta: Eso = 0.00
siesta: Ext. field = 0.00
siesta: Exch.-corr. = -5794.300663
siesta: Ion-electron = -76563.859626
siesta: Ion-ion = 15629.924971
siesta: Ekinion = 0.00
siesta: Total = -19529.842848
siesta: Fermi = -4.707019

siesta: Atomic forces (eV/Ang):
siesta: 1 -0.026727 0.000182 -0.015051
siesta: 2 0.044114 -0.043744 -0.001681
siesta: 3 0.020104 -0.007544 -0.115776
siesta: 4 0.054796 -0.053486 -0.025071
…
…
siesta: 129 -0.036863 -0.041463 -0.047218
siesta: 130 -0.012952 -0.089863 0.127418
siesta: 131 0.020422 0.101546 -0.046036
siesta: 132 0.047941 -0.009764 0.000107
siesta: 133 -0.043814 -0.020094 -0.131299
siesta: 134 -0.056622 0.062521 0.031526
siesta: 135 0.042265 -0.027729 -0.004018


I wonder why it didnt complete Atomic Forces for Atom number:136-138!

A completed output is also attached, and pls note that I used PSP flles
from Simune and
PAO information from the forum.

I hope Siesta users can suggest an indication in this error log.

Was it a Memory Problem? (I have 4+GB RAM free while running this
calculation as I can
see from top command)

Thanks in advance

Krishna

/

INPUT

/
SystemName zif67optical
SystemLabel zif67optical

NumberOfSpecies 4
NumberOfAtoms 138
%block ChemicalSpeciesLabel
1 27 Co
2 7 N
3 6 C
4 1 H
%endblock ChemicalSpeciesLabel

PAO.BasisSize DZP
PAO.BasisType split
PAO.EnergyShift 0.02 Ry
XC.Functional GGA
XC.Authors PBE

kgrid.Cutoff 0. Bohr # Gamma only, didnt work (use this OR below one)
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack

MinSCFIterations 3
MaxSCFIterations 1000
MeshCutoff 350 Ry
DM.MixingWeight 0.025
SCF.Mixer.History 6 # replace DM.NumberPulay
scf.Mixer.Variant GR
scf.Mixer.Kick 3
DM.Tolerance 0.001
XC.functional GGA
XC.authors PBE
SolutionMethod diagon
ElectronicTemperature 300 K

optical
OpticalCalculation .true.
%block Optical.Mesh
12 12 12
%endblock Optical.Mesh
Optical.OffsetMesh .true.
Optical.PolarizationType polarized

Optical.Scissor 0.45 eV
%block Optical.Vector
1.0 0.0 0.0
%endblock Optical.Vector
Optical.Broaden 0.2 eV
Optical.EnergyMaximum 20.0 eV # before it was 5 eV
Optical.EnergyMinimum 0.0 eV

dont use the below setting
#Optical.EnergyMaximum 3.12 eV
#Optical.EnergyMinimum 1.50 eV

%block PAO.Basis
Co 3 0.0
n=4 0 2 E 150.0 4.5
6.5 4.5
1.0 1.0
n=4 1 1 E 100.0 4.5
6.5
1.0
n=3 2 2 E 100.0 4.5
6.5 4.5
1.0 1.0
N 3
n=2 0 2 E 40 -0.9
6.5 4.3806496
n=2 1 2 E 40 -0.9
6.71294063991 2.4269315
n=2 2 1 E 40 -0.9 Q 8.2241579 .010
6.71294063991
C 3
n=2 0 2 E 40 -0.9
5.94869034392 2.5090419
n=2 1 2 E 40 -0.9
7.63838693570 2.6226139
n=2 2 1 E 40 -0.9 Q 6.4005365 .010
7.63838693570
H 2
n=1 0 2 E 10 -0.7
10.0 5.0
n=1 1 1 E 10 -0.7 Q 2.0 1.0
10.0
%endblock PAO.Basis

step 0.00625 bohr
LatticeConstant 1 Ang
%block LatticeVectors
14.343458 0.226118 0.414646
-4.567967 13.577006 0.405857
-4.549189 -6.430382 11.941912
%endblock LatticeVectors

[SIESTA-L] [***Posible SPAM***] Optical Spectrum of Zeolite - not completing

[Krishna Mohan]

Dear List

I am trying to calculate the optical spectrum of a Zeolite compound and we
have its experimental spectrum and it shows a clear absorption in Visible
region (and the pure Zeolite compound is a colored one). So we expect that
the Siesta’s spectrum would reflect this too.
But
when I tried the calculation (Pls see below part) it runs and completed SCF
cycle and it seems it stuck in the portion:

130
-0.012952 -0.089863 0.127418
131 0.020422 0.101546 -0.046036
132 0.047941 -0.009764 0.000107
133 -0.043814 -0.020094 -0.131299
134 -0.056622 0.062521 0.031526
135 0.042265 -0.027729 -0.004018
136 -0.016008 0.021773 0.020389
137 0.063636 -0.039750 -0.033829
138 0.055053 0.033202 -0.021522
Tot
-0.005242 0.008209 -0.009872
Max
0.337362
Res 0.065680 sqrt( Sum f_i^2 / 3N )

Max 0.337362 constrained

Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 2.89 2.86 1.82 -0.46 -0.58 -0.51
(Free)E + p*V (eV/cell) -19533.6875
Target enthalpy (eV/cell) -19529.8878

coxmol: Writing XMOL coordinates into file zif67optical.xyz

siesta: Program’s energy decomposition (eV):
siesta: Ebs = -5482.245303
siesta: Eions = 23083.627097
siesta: Ena = 3227.550941
siesta: Ekin = 16297.878613
siesta: Enl = -9828.161993
siesta: Eso = 0.00
siesta: Edftu = 0.00
siesta: DEna = -413.734991
siesta: DUscf = 64.552342
siesta: DUext = 0.00
siesta: Exc = -5794.300663
siesta: eta*DQ = 0.00
siesta: Emadel = 0.00
siesta: Emeta = 0.00
siesta: Emolmec = 0.00
siesta: Ekinion = 0.00
siesta: Eharris = -19529.842846
siesta: Etot = -19529.842848
siesta: FreeEng = -19529.887822

siesta: Final energy (eV):
siesta: Band Struct. = -5482.245303
siesta: Kinetic = 16297.878613
siesta: Hartree = 30900.513857
siesta: Edftu = 0.00
siesta: Eso = 0.00
siesta: Ext. field = 0.00
siesta: Exch.-corr. = -5794.300663
siesta: Ion-electron = -76563.859626
siesta: Ion-ion = 15629.924971
siesta: Ekinion = 0.00
siesta: Total = -19529.842848
siesta: Fermi = -4.707019
siesta:
Atomic forces (eV/Ang):
siesta: 1 -0.026727 0.000182 -0.015051
siesta: 2 0.044114 -0.043744 -0.001681
siesta: 3 0.020104 -0.007544 -0.115776
siesta: 4 0.054796 -0.053486 -0.025071
…
…
siesta: 129 -0.036863 -0.041463 -0.047218
siesta: 130 -0.012952 -0.089863 0.127418
siesta: 131 0.020422 0.101546 -0.046036
siesta: 132 0.047941 -0.009764 0.000107
siesta: 133 -0.043814 -0.020094 -0.131299
siesta: 134 -0.056622 0.062521 0.031526
siesta: 135 0.042265 -0.027729 -0.004018
--

I wonder why it didnt complete Atomic Forces for Atom number:136-138!

A completed output is also attached, and pls note that I used PSP flles
from Simune and
PAO information from the forum.

*I hope Siesta users can suggest an indication in this error log.*
nohup.zip

(16.1

[SIESTA-L] [***Posible SPAM***] Phonons for MoS2 and WS2

[andreea . nila]

Dear Siesta users,

I am having trouble getting the active IR vibrational modes for MoS2 and 
WS2. More precisely, the phononic modes that the program generates for 
me are up to frequencies of 450 cm-1. But in the literature, the 
experimental IR vibrational modes are in the range 600-3000 cm-1. Why 
can't I get these vibrational modes or what could I change in the fdf 
file to get vibrational modes at higher frequencies?


Thank you!

SystemName MoS2
SystemLabel MoS2
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 16 S
2 42 Mo
%endblock ChemicalSpeciesLabel

NumberOfAtoms 18

LatticeConstant 1.8897268778 Bohr

%block LatticeVectors
9.576720   0.00   0.00
-1.596120   2.764561   0.00
0.00   0.00   13.378290
%endblock LatticeVectors

AtomicCoordinatesFormat NotScaledCartesianBohr

%block AtomicCoordinatesAndAtomicSpecies
-3.0169018247 1.7418097833 6.3203288007 2
-6.0317907678 3.4824553391 18.9609853909   2
-3.0165598445 1.7416118882 16.0098457586   1
-6.0321327480 3.4826534433 9.2714681802 1
-3.0165597841 1.7416118882 21.9121257817   1
-6.0321328083 3.4826534433 3.3691889156 1
3.0155599036 1.7418097833 6.3203288007  2
0.0006709606 3.4824553391 18.96098539092
3.0159018839 1.7416118882 16.00984575861
0.0003289803 3.4826534433 9.2714681802  1
3.0159019442 1.7416118882 21.91212578171
0.0003289200 3.4826534433 3.3691889156  1
9.0480216319 1.7418097833 6.3203288007  2
6.0331326889 3.4824553391 18.96098539092
9.0483636122 1.7416118882 16.00984575861
6.0327907086 3.4826534433 9.2714681802  1
9.0483636725 1.7416118882 21.91212578171
6.0327906483 3.4826534433 3.3691889156  1
%endblock AtomicCoordinatesAndAtomicSpecies

MD.TypeOfRun FC
MD.FCfirst 7
MD.FClast 12
MD.FCdispl 0.04 Bohr

PAO.BasisSize DZP

MeshCutoff 200 Ry

%block kgrid_Monkhorst_Pack
5 0 0 0.5
0 5 0 0.5
0 0 1 0.5
%endblock kgrid_Monkhorst_Pack

%block BandLines
1 0.00 0.00 0.0 \Gamma
20 0.50 0.00 0.0 M
30 0.33 0.33 0.0 K
20 0.00 0.00 0.0 \Gamma
%endblock BandLines

BornCharge true

%block PolarizationGrids
10 4 4
4 10 4
4 4 10
%endblock PolarizationGrids

XC.Functional LDA
XC.Authors CA

DM.NumberPulay 5
DM.MixingWeight 0.01
DM.Tolerance 1.d-5

MaxSCFIterations 1000
-- 
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***] SUBSCRIBE SIESTA-L

[zahra Sartipi]

-- 
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***] about the master version of siesta

[Bo Xiao]

Dear user

The mater version of siesta support the psml potental and contain all the 
features of V4.1+, while it is a developed version.
I am wondering whether the results obtained from this mater version is all 
right, and publish paper.

Thanks!

-- 
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***] about the method to obtain the pseudo potentials

[Bo Xiao]

Dear users,

As i know, there are several methods to obtain the pseudo potentials, while i 
am wondering whcih one is recommanded or safe.

  1.   I konw the best method is by using the ATOM package, while its input 
file and the subsquent test procedure is sometimes difficult to deal with.
  2.  I can download the pseudo potential from  
PseudoDojo with .psml format. Then, by using the psml2psf coverter,
with the command line: psml2psf -o Hf.psf Hf.psml, the Hf.psf was obtained. 
When using Hf.psf, i still need to include the electron state in the PAO.basis 
part in the .fdf input file.
Is it possible to fullfill the PAO.basis part automatically? is this method 
safe?
In this website 
https://urldefense.com/v3/__https://www.simuneatomistics.com/siesta-pro/siesta-pseudos-and-basis-database/__;!!D9dNQwwGXtA!QLKbXiqFrfXQs1wLG_i4QTrGWgPTC8rqyYYDrWSXBsqsJxwzcrQe2OYDgn1EyCayVNKDaAROBZOkeqcmMaQ$
 , it provied the pseudo potentials of limited elements together with the 
corrponding PAO.basis part.

   3. Obtain the pseudo potential with .psf directly from here  
https://departments.icmab.es/leem/SIESTA_MATERIAL/Databases/Pseudopotentials/periodictable-gga-abinit.html,
 the PAO.basis part is included.
Is there any method to obtain the pseudo potentials?

Thanks!

-- 
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***] RE: number of k-points in denchar

[Fanmiao Kong]

Dear Rajesh,

Sorry I have no idea about this error. I would also like to know if someone 
else can provide a solution.

Best,
Fanmiao

Fanmiao Kong
Department of Materials, Trinity College, University of Oxford
Tel: +44 (0)7529931806 / +86 13162054601
16 Parks Road, OX1 3PH, Oxford, UK

-Original Message-
From: Rajesh_Dutta  
Sent: 2022年9月7日 14:50
To: Fanmiao Kong ; siesta-l@uam.es
Subject: Re: [SIESTA-L] [***Posible SPAM***] RE: number of k-points in denchar

Dear Fanmiao,

Many thanks for the information, I exactly needed thatinfo.
BTW, I was playing with different PP format (.psf and .psml) to have a test on 
result. Mg.psml downloaded from pseudo dojo through some following error:
**
 POLgen: Perturbative polarization orbital with L=  1

POLgen: Polarization orbital for state 3s
 POLARIZATION: Iteration to find the polarization  orbital has failed !
sys::die: Program terminated
Stopping Program from Node:0
 Please try with a Rc no bigger than2.1037069778585620   Bohr
sys::die: Program terminated
Stopping Program from Node:0
**

I guess I can not modify the downloaded psml file with smaller Rc as suggested 
by the program.

Is there any way to modify or any input that I can give inside the Siesta to 
fix this error?

Thanks and best regards,
Rajesh


-- 
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***] RE: number of k-points in denchar

[Rajesh_Dutta]

Dear Fanmiao,

Many thanks for the information, I exactly needed thatinfo.
BTW, I was playing with different PP format (.psf and .psml) to have a test on
result. Mg.psml downloaded from pseudo dojo through some following error:
**
 POLgen: Perturbative polarization orbital with L=  1

POLgen: Polarization orbital for state 3s
 POLARIZATION: Iteration to find the polarization
 orbital has failed !
sys::die: Program terminated
Stopping Program from Node:0
 Please try with a Rc no bigger than2.1037069778585620   Bohr
sys::die: Program terminated
Stopping Program from Node:0
**

I guess I can not modify the downloaded psml file with smaller Rc as suggested
by the program.

Is there any way to modify or any input that I can give inside the Siesta to
fix this error?

Thanks and best regards,
Rajesh


-- 
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***] RE: number of k-points in denchar

[Fanmiao Kong]

Dear Rajesh,

For your first question, I think if you plot the wavefunction from 
SystemLabel.bands.WFSX, then the answer is yes. The program Denchar plot the 
wavefunctions of selected bands (controlled by options: WFS.Write.For.Bands, 
WFS.Band.Min, WFS.Band.Max) for all the k points that you specify in %block 
BandLines. In the SystemLabel.bands file there is same number of k points. 

Of course you can reduce the number of k points by using %block 
WaveFuncKPoints. Then you use denchar and plot the data from 
SystemLabel.selected.WFSX (cp SystemLabel.selected.WFSX SystemLabel.WFSX). I 
don't think this option will affect the charge density in SystemLabel.RHO file. 

Kind regards,

Fanmiao

Fanmiao Kong
Department of Materials, Trinity College, University of Oxford
Tel: +44 (0)7529931806 / +86 13162054601
16 Parks Road, OX1 3PH, Oxford, UK

-Original Message-
From: siesta-l-requ...@uam.es  On Behalf Of 
Rajesh_Dutta
Sent: 06 September 2022 09:56
To: siesta-l@uam.es
Subject: [SIESTA-L] number of k-points in denchar

Dear Siesta members and expert users,
I am computing electron density using Denchar and it says "Generating values of 
wavefunction on the grid for k-point ##" Is this number of k-points same as 
written in SystemLabel.bands file? Is it the number given in %block BandLines?
What if I calculate for some selected bandlines to reduce this k-point number 
using SystemLable.selected.WFSX, will it give me the complete charge density?
Your help and suggestions would be highly appreciated.

-Rajesh

-- 
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***] Re:

[Amal Yassin]

Hi
How can make an Access to the executable File, typically located in the
Filder./obj ?
Best regard.


Amal Yassin  schrieb am So., 31. Juli 2022, 18:07:

> Hello all,
>
> I have downloaded an Atom program, but some Atoms are not in it, How do I get 
> their PSf file?!
>
>
>

-- 
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***]

[Amal Yassin]

Hello all,

I have downloaded an Atom program, but some Atoms are not in it, How
do I get their PSf file?!

-- 
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

[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/)

Re: [SIESTA-L] [***Posible SPAM***]Re: Nanoribbon Band Structure

[Ziba Torkashvand]

Thank you for the clarification but the resulted band structure is no
longer have similarity to the previous one, although I have tested
everything but just some intersecting lines. I would be grateful if you
take a look at my fdf.

Best,
Ziba Toorkashvand

[image: Mailtrack]

Sender
notified by
Mailtrack

09/10/19,
01:55:24 AM

On Tue, Sep 10, 2019 at 12:36 AM Nick Papior  wrote:

> When you duplicate a system you fold the bandstructure. However, they
> refer to the same system in a new reference supercell.
> If you *only* duplicate your system you should be able to *visually*
> decipher which bands belongs to the original band-structure by following
> the folding.
>
> Den søn. 8. sep. 2019 kl. 22.10 skrev Ziba Torkashvand <
> zi.torkashv...@gmail.com>:
>
>> Dear Siesta users, I want to do a calculation for armchair boron nitride.
>> First, I calculated the band structure for a H-terminated 16-atom
>> supercell and everything goes well but after repeating it in the
>> Z-direction the band structure is completely different. Below is my input
>> data.
>> Any help will be kindly appreciated.
>>
>> SystemName  BN96
>> SystemLabel BN96
>>
>> NumberOfAtoms  120
>> NumberOfSpecies3
>>
>> %block ChemicalSpeciesLabel
>>   1   5  B
>>   2   7  N
>>   3   1  H
>> %endblock ChemicalSpeciesLabel
>>
>> %block PAO.BasisSizes
>> B  DZP
>> N  DZP
>> H  DZP
>> %endblock PAO.BasisSizes
>> XC.functional GGA
>> XC.authorsPBE
>>
>> LatticeConstant 1.00 Ang
>> %block LatticeVectors
>> 15.0184160.000   
>> 28.110748   
>> 0   26.254219
>> %endblock LatticeVectors
>>
>> AtomicCoordinatesFormat Ang
>> %block AtomicCoordinatesAndAtomicSpecies
>> 4.99806814   10.130305692.89878885   1   1  B
>> 4.99801199   11.373707333.63699571   2   2  N
>> 4.99813743   10.164713141.48289328   2   3  N
>> 4.99812179   11.384041660.71785760   1   4  B
>> 4.99804236   12.633718302.90545729   1   5  B
>> 4.99806374   13.890267583.63634513   2   6  N
>> 4.99806280   12.638727501.44914602   2   7  N
>> 4.99813944   13.894167510.71724054   1   8  B
>> 4.99808119   15.144938502.90508953   1   9  B
>> 4.99803141   16.400463363.63686499   2  10  N
>> 4.99813910   15.148881461.44842366   2  11  N
>> 4.99812876   16.405596150.71755851   1  12  B
>> 4.99798906   17.655337962.90555046   1  13  B
>> 4.99788191   18.874674913.67055732   2  14  N
>> 4.99805568   17.665741481.44897236   2  15  N
>> 4.99801717   18.909319740.71071300   1  16  B
>> 4.998065039.036779713.45950287   3  17  H
>> 4.998160339.283326440.96932716   3  18  H
>> 4.99786641   19.756247713.15723011   3  19  H
>> 4.99796237   20.002838491.27139448   3  20  H
>> 4.99790820   10.130268257.27450101   1  21  B
>> 4.99785143   11.373665938.01269652   2  22  N
>> 4.99797713   10.164653175.85858366   2  23  N
>> 4.99796310   11.384015545.09356218   1  24  B
>> 4.99788147   12.633680777.28115248   1  25  B
>> 4.99790238   13.890227018.01205439   2  26  N
>> 4.99790265   12.638677345.82484688   2  27  N
>> 4.99797974   13.894131905.09294272   1  28  B
>> 4.99792079   15.144893967.28078063   1  29  B
>> 4.99787292   16.400430228.01257295   2  30  N
>> 4.99797938   15.148843905.82412986   2  31  N
>> 4.99796881   16.405551425.09325906   1  32  B
>> 4.99782955   17.655303327.28124601   1  33  B
>> 4.99772085   18.874612468.04627489   2  34  N
>> 4.99789629   17.665708825.82467266   2  35  N
>> 4.99785742   18.909277735.08641847   1  36  B
>> 4.997905129.036738627.83520640   3  37  H
>> 4.998000359.283297295.34504337   3  38  H
>> 4.99770663   19.756228767.53291210   3  39  H
>> 4.99780259   20.002804865.64709520   3  40  H
>> 4.99774776   10.13022465   11.65017932   1  41  B
>> 4.99769162   11.37362315   12.38839710   2  42  N
>> 4.99781561   10.16464145   10.23430424   2  43  N
>> 4.99780189   11.383968029.46925765   1  44  B
>> 4.99772147   12.63364075   11.65685073   1  45  B
>> 4.99774209   13.89018391   12.38775530   2  46  N
>> 4.99774334   12.63863840   10.20055561   2  47  N
>> 4.99781899   13.894093229.46863329   1  48  B
>> 4.99776070   15.14485300   11.65647996   1  49  B
>> 4.99771319   16.40038834   12.38827319   2  50  N
>> 

[SIESTA-L] [***Posible SPAM***]Re: Nanoribbon Band Structure

[Nick Papior]

When you duplicate a system you fold the bandstructure. However, they refer
to the same system in a new reference supercell.
If you *only* duplicate your system you should be able to *visually*
decipher which bands belongs to the original band-structure by following
the folding.

Den søn. 8. sep. 2019 kl. 22.10 skrev Ziba Torkashvand <
zi.torkashv...@gmail.com>:

> Dear Siesta users, I want to do a calculation for armchair boron nitride.
> First, I calculated the band structure for a H-terminated 16-atom
> supercell and everything goes well but after repeating it in the
> Z-direction the band structure is completely different. Below is my input
> data.
> Any help will be kindly appreciated.
>
> SystemName  BN96
> SystemLabel BN96
>
> NumberOfAtoms  120
> NumberOfSpecies3
>
> %block ChemicalSpeciesLabel
>   1   5  B
>   2   7  N
>   3   1  H
> %endblock ChemicalSpeciesLabel
>
> %block PAO.BasisSizes
> B  DZP
> N  DZP
> H  DZP
> %endblock PAO.BasisSizes
> XC.functional GGA
> XC.authorsPBE
>
> LatticeConstant 1.00 Ang
> %block LatticeVectors
> 15.0184160.000   
> 28.110748   
> 0   26.254219
> %endblock LatticeVectors
>
> AtomicCoordinatesFormat Ang
> %block AtomicCoordinatesAndAtomicSpecies
> 4.99806814   10.130305692.89878885   1   1  B
> 4.99801199   11.373707333.63699571   2   2  N
> 4.99813743   10.164713141.48289328   2   3  N
> 4.99812179   11.384041660.71785760   1   4  B
> 4.99804236   12.633718302.90545729   1   5  B
> 4.99806374   13.890267583.63634513   2   6  N
> 4.99806280   12.638727501.44914602   2   7  N
> 4.99813944   13.894167510.71724054   1   8  B
> 4.99808119   15.144938502.90508953   1   9  B
> 4.99803141   16.400463363.63686499   2  10  N
> 4.99813910   15.148881461.44842366   2  11  N
> 4.99812876   16.405596150.71755851   1  12  B
> 4.99798906   17.655337962.90555046   1  13  B
> 4.99788191   18.874674913.67055732   2  14  N
> 4.99805568   17.665741481.44897236   2  15  N
> 4.99801717   18.909319740.71071300   1  16  B
> 4.998065039.036779713.45950287   3  17  H
> 4.998160339.283326440.96932716   3  18  H
> 4.99786641   19.756247713.15723011   3  19  H
> 4.99796237   20.002838491.27139448   3  20  H
> 4.99790820   10.130268257.27450101   1  21  B
> 4.99785143   11.373665938.01269652   2  22  N
> 4.99797713   10.164653175.85858366   2  23  N
> 4.99796310   11.384015545.09356218   1  24  B
> 4.99788147   12.633680777.28115248   1  25  B
> 4.99790238   13.890227018.01205439   2  26  N
> 4.99790265   12.638677345.82484688   2  27  N
> 4.99797974   13.894131905.09294272   1  28  B
> 4.99792079   15.144893967.28078063   1  29  B
> 4.99787292   16.400430228.01257295   2  30  N
> 4.99797938   15.148843905.82412986   2  31  N
> 4.99796881   16.405551425.09325906   1  32  B
> 4.99782955   17.655303327.28124601   1  33  B
> 4.99772085   18.874612468.04627489   2  34  N
> 4.99789629   17.665708825.82467266   2  35  N
> 4.99785742   18.909277735.08641847   1  36  B
> 4.997905129.036738627.83520640   3  37  H
> 4.998000359.283297295.34504337   3  38  H
> 4.99770663   19.756228767.53291210   3  39  H
> 4.99780259   20.002804865.64709520   3  40  H
> 4.99774776   10.13022465   11.65017932   1  41  B
> 4.99769162   11.37362315   12.38839710   2  42  N
> 4.99781561   10.16464145   10.23430424   2  43  N
> 4.99780189   11.383968029.46925765   1  44  B
> 4.99772147   12.63364075   11.65685073   1  45  B
> 4.99774209   13.89018391   12.38775530   2  46  N
> 4.99774334   12.63863840   10.20055561   2  47  N
> 4.99781899   13.894093229.46863329   1  48  B
> 4.99776070   15.14485300   11.65647996   1  49  B
> 4.99771319   16.40038834   12.38827319   2  50  N
> 4.99781908   15.14880766   10.19983398   2  51  N
> 4.99780894   16.405511359.46895174   1  52  B
> 4.99766994   17.65526407   11.65694927   1  53  B
> 4.99756106   18.87456680   12.42197812   2  54  N
> 4.99773633   17.66566869   10.20037198   2  55  N
> 4.99769738   18.909243529.46210019   1  56  B
> 4.997745419.03669567   12.21089917   3  57  H
> 4.997840239.283234599.72071812   3  58  H
> 4.99754692   19.75618834   11.90861606   3  59  H
> 4.99764272   20.00276817   10.02279069   3  60  H
> 4.99758812   10.13017685   16.02589674   1  61  B
> 

[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***]<< convergence problems BN+Ni >>

[Salvador Barraza-Lopez]

Indeed, the system is small.

Cheers,

-Salvador


From: siesta-l-requ...@uam.es  on behalf of I. Camps 

Sent: Monday, December 3, 2018 10:08:31 AM
To: siesta-l@uam.es
Subject: Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

Salvador,

The system is 7.83Angs in diameter and 12.78Angs in length. I already worked 
with carbon nanotubes with similar sizes and with the same combinations of 
metals without any problems.

[]'s,

Camps


On Fri, Nov 30, 2018 at 7:08 PM Salvador Barraza-Lopez 
mailto:sbarr...@uark.edu>> wrote:

 This will be a not too specific comment and I have not looked into your atomic 
system, but if your system dimensions are too dissimilar; i.e., if the tube is 
too long, then you have a cycle of charge moving into and out of your Ni atom, 
this process gets larger the longer an asymmetric dimension is. I have seen 
this in multiple systems that have one direction that is, say, orders of 
magnitude larger than the other two. This could be aggravated if the forces are 
too large, this is, if the structural optimization is not very strict.


So I would look at forces first, and maybe approach the Ni atom slowly into the 
tube *by hand*, using the DM from the previous *ionic* step to get you going.


 Hopefully, these comments are useful.


-Salvador


From: siesta-l-requ...@uam.es<mailto:siesta-l-requ...@uam.es> 
mailto:siesta-l-requ...@uam.es>> on behalf of I. Camps 
mailto:ica...@gmail.com>>
Sent: Thursday, November 29, 2018 11:23:50 AM
To: siesta-l@uam.es<mailto:siesta-l@uam.es>
Subject: Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

Dear Leonardo,

Thank you for your advise.

Unfortunately, your suggestions did not work :(

[]'s,

Camps


On Wed, Nov 28, 2018 at 7:04 PM Leonardo Fonseca 
mailto:fonsecal...@gmail.com>> wrote:
You could try a smaller mixing parameter. Currently you are using 
DM.MixingWeight 0.01. You could try 0.005 or even 0.001. If it works then you 
can increase it back to see at which value convergence is lost.

Em ter, 27 de nov de 2018 às 19:02, I. Camps 
mailto:ica...@gmail.com>> escreveu:
Hello SIESTers,

I am starting doing calculations with boron nitride nanotube interacting with 
nickel.

My problem is that SCF calculations are not converging for even 1500 steps!

I am using several mesh cutoff energies (between 150 and 650 Ry) but the 
problem persists.

The input, pseudopotentials and output files are attached to this email (and 
can be download from the link 
https://drive.google.com/open?id=1s3Z-kQWcNptvGMX3pM7dbTR2FpVZLX74<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_open-3Fid-3D1s3Z-2DkQWcNptvGMX3pM7dbTR2FpVZLX74=DwMFaQ=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA=d_wByFh562xnF38KR6av_HxjWbFMw90KK5BKq2dwiQc=8vdXSd45w4M0hHp4CImKWXV-yNpYNLjf6GzeVD2y6A8=yp0Mc62NicI6eDUsFqLpn_757uWL9lVgtOFM-f4-pUU=>).

Any help, ideas are welcome.

Regards,

Camps

Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

[I. Camps]

Salvador,

The system is 7.83Angs in diameter and 12.78Angs in length. I already
worked with carbon nanotubes with similar sizes and with the same
combinations of metals without any problems.

[]'s,

Camps


On Fri, Nov 30, 2018 at 7:08 PM Salvador Barraza-Lopez 
wrote:

>  This will be a not too specific comment and I have not looked into your
> atomic system, but if your system dimensions are too dissimilar; i.e., if
> the tube is too long, then you have a cycle of charge moving into and out
> of your Ni atom, this process gets larger the longer an asymmetric
> dimension is. I have seen this in multiple systems that have one direction
> that is, say, orders of magnitude larger than the other two. This could be
> aggravated if the forces are too large, this is, if the structural
> optimization is not very strict.
>
>
> So I would look at forces first, and maybe approach the Ni atom slowly
> into the tube *by hand*, using the DM from the previous *ionic* step to get
> you going.
>
>
>  Hopefully, these comments are useful.
>
>
> -Salvador
> --
> *From:* siesta-l-requ...@uam.es  on behalf of I.
> Camps 
> *Sent:* Thursday, November 29, 2018 11:23:50 AM
> *To:* siesta-l@uam.es
> *Subject:* Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems
> BN+Ni >>
>
> Dear Leonardo,
>
> Thank you for your advise.
>
> Unfortunately, your suggestions did not work :(
>
> []'s,
>
> Camps
>
>
> On Wed, Nov 28, 2018 at 7:04 PM Leonardo Fonseca 
> wrote:
>
> You could try a smaller mixing parameter. Currently you are using
> DM.MixingWeight 0.01. You could try 0.005 or even 0.001. If it works then
> you can increase it back to see at which value convergence is lost.
>
> Em ter, 27 de nov de 2018 às 19:02, I. Camps  escreveu:
>
> Hello SIESTers,
>
> I am starting doing calculations with boron nitride nanotube interacting
> with nickel.
>
> My problem is that SCF calculations are not converging for even 1500 steps!
>
> I am using several mesh cutoff energies (between 150 and 650 Ry) but the
> problem persists.
>
> The input, pseudopotentials and output files are attached to this email
> (and can be download from the link
> https://drive.google.com/open?id=1s3Z-kQWcNptvGMX3pM7dbTR2FpVZLX74
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_open-3Fid-3D1s3Z-2DkQWcNptvGMX3pM7dbTR2FpVZLX74=DwMFaQ=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA=d_wByFh562xnF38KR6av_HxjWbFMw90KK5BKq2dwiQc=8vdXSd45w4M0hHp4CImKWXV-yNpYNLjf6GzeVD2y6A8=yp0Mc62NicI6eDUsFqLpn_757uWL9lVgtOFM-f4-pUU=>
> ).
>
> Any help, ideas are welcome.
>
> Regards,
>
> Camps
>
>

Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

[Salvador Barraza-Lopez]

 This will be a not too specific comment and I have not looked into your atomic 
system, but if your system dimensions are too dissimilar; i.e., if the tube is 
too long, then you have a cycle of charge moving into and out of your Ni atom, 
this process gets larger the longer an asymmetric dimension is. I have seen 
this in multiple systems that have one direction that is, say, orders of 
magnitude larger than the other two. This could be aggravated if the forces are 
too large, this is, if the structural optimization is not very strict.


So I would look at forces first, and maybe approach the Ni atom slowly into the 
tube *by hand*, using the DM from the previous *ionic* step to get you going.


 Hopefully, these comments are useful.


-Salvador


From: siesta-l-requ...@uam.es  on behalf of I. Camps 

Sent: Thursday, November 29, 2018 11:23:50 AM
To: siesta-l@uam.es
Subject: Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

Dear Leonardo,

Thank you for your advise.

Unfortunately, your suggestions did not work :(

[]'s,

Camps


On Wed, Nov 28, 2018 at 7:04 PM Leonardo Fonseca 
mailto:fonsecal...@gmail.com>> wrote:
You could try a smaller mixing parameter. Currently you are using 
DM.MixingWeight 0.01. You could try 0.005 or even 0.001. If it works then you 
can increase it back to see at which value convergence is lost.

Em ter, 27 de nov de 2018 às 19:02, I. Camps 
mailto:ica...@gmail.com>> escreveu:
Hello SIESTers,

I am starting doing calculations with boron nitride nanotube interacting with 
nickel.

My problem is that SCF calculations are not converging for even 1500 steps!

I am using several mesh cutoff energies (between 150 and 650 Ry) but the 
problem persists.

The input, pseudopotentials and output files are attached to this email (and 
can be download from the link 
https://drive.google.com/open?id=1s3Z-kQWcNptvGMX3pM7dbTR2FpVZLX74<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_open-3Fid-3D1s3Z-2DkQWcNptvGMX3pM7dbTR2FpVZLX74=DwMFaQ=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA=d_wByFh562xnF38KR6av_HxjWbFMw90KK5BKq2dwiQc=8vdXSd45w4M0hHp4CImKWXV-yNpYNLjf6GzeVD2y6A8=yp0Mc62NicI6eDUsFqLpn_757uWL9lVgtOFM-f4-pUU=>).

Any help, ideas are welcome.

Regards,

Camps

Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

[I. Camps]

Dear Leonardo,

Thank you for your advise.

Unfortunately, your suggestions did not work :(

[]'s,

Camps


On Wed, Nov 28, 2018 at 7:04 PM Leonardo Fonseca 
wrote:

> You could try a smaller mixing parameter. Currently you are using
> DM.MixingWeight 0.01. You could try 0.005 or even 0.001. If it works then
> you can increase it back to see at which value convergence is lost.
>
> Em ter, 27 de nov de 2018 às 19:02, I. Camps  escreveu:
>
>> Hello SIESTers,
>>
>> I am starting doing calculations with boron nitride nanotube interacting
>> with nickel.
>>
>> My problem is that SCF calculations are not converging for even 1500
>> steps!
>>
>> I am using several mesh cutoff energies (between 150 and 650 Ry) but the
>> problem persists.
>>
>> The input, pseudopotentials and output files are attached to this email
>> (and can be download from the link
>> https://drive.google.com/open?id=1s3Z-kQWcNptvGMX3pM7dbTR2FpVZLX74).
>>
>> Any help, ideas are welcome.
>>
>> Regards,
>>
>> Camps
>>
>>

Re: [SIESTA-L] [***Posible SPAM***]<< convergence problems BN+Ni >>

[Leonardo Fonseca]

You could try a smaller mixing parameter. Currently you are using
DM.MixingWeight 0.01. You could try 0.005 or even 0.001. If it works then
you can increase it back to see at which value convergence is lost.

Em ter, 27 de nov de 2018 às 19:02, I. Camps  escreveu:

> Hello SIESTers,
>
> I am starting doing calculations with boron nitride nanotube interacting
> with nickel.
>
> My problem is that SCF calculations are not converging for even 1500 steps!
>
> I am using several mesh cutoff energies (between 150 and 650 Ry) but the
> problem persists.
>
> The input, pseudopotentials and output files are attached to this email
> (and can be download from the link
> https://drive.google.com/open?id=1s3Z-kQWcNptvGMX3pM7dbTR2FpVZLX74).
>
> Any help, ideas are welcome.
>
> Regards,
>
> Camps
>
>

[SIESTA-L] [***Posible SPAM***]Re: << SIESTA wavefunction -> Multiwfn >>

[Cina Foroutan-Nejad]

Dear Camps,
I recommend to contact Todd A. Keith, the developer of AIMAll. I know he is 
keen to develop his code to be able to analyze any type of basis set. 
Respectfully yours,Cina

Sent from Yahoo Mail on Android 
 
  On Thu, 23 Aug 2018 at 22:02, I. Camps wrote:   Hi Peter,
Yeah, unfortunately, Multiwfn needs the wavefunctions in Gassian form.
 
Here is the comment of Multiwfn developer:


Dear Camps,

Unfortunately, this cannot be easily realized. AFAIK, Siesta employs numerical 
basis set, however, to carry out wavefunction analysis in Multiwfn, the 
wavefunction must be represented by Gaussian type functions (GTFs).

Best regards,

Tian
 
[]'s,

Camps


On Tue, Aug 21, 2018 at 5:01 PM Peter Koval  wrote:

http://sobereva.com/multiwfn/

It seems there are only Gaussian orbitals in the data files? No?
On Wed, Aug 15, 2018 at 10:05 PM I. Camps  wrote:
>
> Hello SIESTers,
>
> I was wondering if there is any tool that can convert the wavefunction file 
> obtained from SIESTA to a format recognized by Multiwfn software 
> (http://sobereva.com/multiwfn/).
>
> Multiwfn is a free extremely powerful program for realizing electronic 
> wavefunction analysis.
>
> []'s,
>
> Camps

  

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

Re: [SIESTA-L] [***Posible SPAM***]2

[Mayuri Vaghela]

to obtain projected density graph you should use fmpdos utility from utils
 after getting *.PDOS file.
go to terminal and enter ./fmpdos, then in terminal output file name will
be asked give that name as pdos.dat again it will ask the atom symbol of
which you want to PDOS gaph and also give for which orbital state you need
PDOS.
for example IF YOU WANT PDOS FOR 2P.
then n=2
   l=1
   m=9 for all m.


On Mon, Jul 25, 2016 at 8:34 AM, 懒人的冥想  wrote:

> Dear all.
>   As a beginner,I donot know how to get the graph by using .PDOS
> and .RHO file which come from the result of siesta.I hope for your hlep.
> Notions,I should use rho2xsf  to get .XSF file for .RHO file ,and
> then use XCRYSDEN to get my graph,but how to 0perate?moreover,for .PDOS
> file,what should I do?
>

[SIESTA-L] [***Posible SPAM***]2

[??????????]

Dear all.
  As a beginner,I donot know how to get the graph by using .PDOS and 
.RHO file which come from the result of siesta.I hope for your hlep.
Notions,I should use rho2xsf  to get .XSF file for .RHO file ,and then 
use XCRYSDEN to get my graph,but how to 0perate?moreover,for .PDOS file,what 
should I do?

[SIESTA-L] [***Posible SPAM***]2

[????]

Dear all.
   As a beginner,I donot know how to get the graph by using .PDOS and 
.RHO file which come from the result of siesta.I hope for your hlep.
 Notions,I should use rho2xsf  to get .XSF file for .RHO file ,and then 
use XCRYSDEN to get my graph,but how to 0perate?moreover,for .PDOS file,what 
should I do?

[SIESTA-L] [***Posible SPAM***]Re: siesta

[Zeila Zanolli]

Hi,

you edit the gnubands fortran code and increase the corresponding
number (for example, number of bands). Recompile and enjoy.

Cheers
Z
---
Dr. Zeila Zanolli

RWTH Aachen, Institute for Theoretical Solid State Physics
ETSF Research Team Leader (http://www.etsf.eu/)

Mobile: +32 487 556699
Office (RWTH): +49 241 80 27030
Office (ULg): +32 (0)4 366 3636
e-mail: zeilazano...@gmail.com
web: http://zeilazanolli.wordpress.com/home
ResearcherID: http://www.researcherid.com/rid/F-9568-2010

Announcements:
21st ETSF Workshop on Electronic Excitations:
Dynamics and spectroscopy of correlated systems
19 - 23 September 2016, Lund, Sweden
website: https://workshop.etsf.eu/

NanoteC16
Carbon Nanoscience and Nanotechnology
31 August - 03 September 2016, Trinity College Dublin, Dublin, Ireland
website: http://nanotec-conference.net/



On Mon, Jun 27, 2016 at 10:48 AM, 木材  wrote:
> when I deal with the computed result of siesta and  input order
> "gnubands",it show that
> Dimensions  in gnubands too small. how should I do to solve the problem,I
> hope for geting your help

Re: [SIESTA-L] [***Posible SPAM***]2

[Nick Papior]

Gnu 4.8.5 is compliant with siesta and you should have no problems
using that compiler.

Regarding the error message:
Have you tried some of the test systems to ensure that you do not have
a buggy installation?

2016-04-06 13:50 GMT+02:00 Suman deep :
> Sir i have used compiler version 4.8.5 for siesta installation, but it is
> still not working
> and using intel fortran compiler i was able to install sieata-4.0b-485, but
> when i tried to run a simple program it just stopped giving error as;
>
> Failure to converge standard eigenproblem
> Stopping Program from Node:0
> abort: Fortran Abort Called
>
>
> Please suggest some solution.



-- 
Kind regards Nick

[SIESTA-L] [***Posible SPAM***]2

[Suman deep]

Sir i have used compiler version 4.8.5 for siesta installation, but it is
still not working
and using intel fortran compiler i was able to install sieata-4.0b-485, but
when i tried to run a simple program it just stopped giving error as;

Failure to converge standard eigenproblem
Stopping Program from Node:0
abort: Fortran Abort Called


Please suggest some solution.

[SIESTA-L] [***Posible SPAM***]2

[arash ghafary]

Hi,
If everyone know how to use fatbands in spin-ploarized systems,i.e.,
fatbands for up and down orbital bands, help me.
For total bands I know by using  new.gnubands -s 1 , up and down bands are
separated. But for fatbands I have problem.
Thanks

Re: [SIESTA-L] [***Posible SPAM***]2

[Nick Papior]

I have never had any problems with new.gnubands So you have to be
more specific than that...

2016-03-22 5:51 GMT+01:00 Farzaneh Farzadi :
> Dear Nick
>
> I tried the new.gnubands...
> but it did not work!
>
> "STOP Dimensions in gnubands too small"
>
>
> On Mon, Mar 21, 2016 at 1:13 PM, Nick Papior  wrote:
>>
>> Try the new.gnubands executable instead.
>>
>> --
>>
>> Kind regards Nick Papior
>>
>> On 21 Mar 2016 06:11, "Farzaneh Farzadi"  wrote:
>>>
>>> Dear users
>>>
>>>  I want to plot the bandstructure of siesta results with the following
>>> command:
>>>
>>> "gfortran -o gnubands.x gnubands.f
>>> ./gnubands.x < systemlabel.bands > systemlabels.bands.gnuplot.dat
>>> xmgrace -nxy systemlabels.bands.gnuplot.dat"
>>>
>>> unfortunately, the systemlabels.bands.gnnuplot.dat is empty and a screen
>>> appears indicating the following text:
>>>
>>> "STOP Dimensions in gnubands too small"
>>>
>>> Please kindly help me solve this problem.
>>> Regards
>>>
>



-- 
Kind regards Nick

Re: [SIESTA-L] [***Posible SPAM***]2

[Farzaneh Farzadi]

Dear Nick

I tried the new.gnubands...
but it did not work!

"STOP Dimensions in gnubands too small"


On Mon, Mar 21, 2016 at 1:13 PM, Nick Papior  wrote:

> Try the new.gnubands executable instead.
>
> --
>
> Kind regards Nick Papior
> On 21 Mar 2016 06:11, "Farzaneh Farzadi"  wrote:
>
>> Dear users
>>
>>  I want to plot the bandstructure of siesta results with the following
>> command:
>>
>> "gfortran -o gnubands.x gnubands.f
>> ./gnubands.x < systemlabel.bands > systemlabels.bands.gnuplot.dat
>> xmgrace -nxy systemlabels.bands.gnuplot.dat"
>>
>> unfortunately, the systemlabels.bands.gnnuplot.dat is empty and a screen
>> appears indicating the following text:
>>
>> "STOP Dimensions in gnubands too small"
>>
>> Please kindly help me solve this problem.
>> Regards
>>
>>

Re: [SIESTA-L] [***Posible SPAM***]2

[Nick Papior]

Try the new.gnubands executable instead.

--

Kind regards Nick Papior
On 21 Mar 2016 06:11, "Farzaneh Farzadi"  wrote:

> Dear users
>
>  I want to plot the bandstructure of siesta results with the following
> command:
>
> "gfortran -o gnubands.x gnubands.f
> ./gnubands.x < systemlabel.bands > systemlabels.bands.gnuplot.dat
> xmgrace -nxy systemlabels.bands.gnuplot.dat"
>
> unfortunately, the systemlabels.bands.gnnuplot.dat is empty and a screen
> appears indicating the following text:
>
> "STOP Dimensions in gnubands too small"
>
> Please kindly help me solve this problem.
> Regards
>
>

[SIESTA-L] [***Posible SPAM***]2

[Farzaneh Farzadi]

Dear users

 I want to plot the bandstructure of siesta results with the following
command:

"gfortran -o gnubands.x gnubands.f
./gnubands.x < systemlabel.bands > systemlabels.bands.gnuplot.dat
xmgrace -nxy systemlabels.bands.gnuplot.dat"

unfortunately, the systemlabels.bands.gnnuplot.dat is empty and a screen
appears indicating the following text:

"STOP Dimensions in gnubands too small"

Please kindly help me solve this problem.
Regards

Re: [SIESTA-L] [***Posible SPAM***]2

[Farzaneh Farzadi]

Thank you for your valuable suggestion.

On Sat, Mar 19, 2016 at 2:06 AM, Nick Papior  wrote:

> Fatal Error: Cannot read module file ‘flib_sax.mod’ opened at (1),
> because it was created by a different version of GNU Fortran
> compilation terminated.
>
> Do make clean...
>
> 2016-03-18 16:57 GMT+01:00 Farzaneh Farzadi :
> > Dear users
> >
> > I'm a new user of SIESTA code (siesta-3.2 version). Please help me with
> the
> > following trouble:
> >  I need the Pdosxml executive file to draw .PDOS, but this executive
> file is
> > not created in pdosxml folder via "make" command and a screen appears
> > indicating the following error:
> >
> > "Making sure that the xmlparser library is compiled...
> > (cd ../../Obj/xmlparser ; make "VPATH=../../Src/xmlparser")
> > make[1]: Entering directory
> > '/home/farzadi/pakage/siesta-3.2-pl-5/Obj/xmlparser'
> > make[1]: Nothing to be done for 'module'.
> > make[1]: Leaving directory
> > '/home/farzadi/pakage/siesta-3.2-pl-5/Obj/xmlparser'
> > f95  -c -g -O2  -I../../Obj/xmlparserm_pdos.f90
> > m_pdos.f90:13:4:
> >  use flib_sax
> >1
> > Fatal Error: Cannot read module file ‘flib_sax.mod’ opened at (1),
> because
> > it was created by a different version of GNU Fortran
> > compilation terminated.
> > ../../Obj/arch.make:66: recipe for target 'm_pdos.o' failed
> > make: *** [m_pdos.o] Error 1"
> >
> > I would be really appreciated if anyone can help me with this problem.
> > Regards
> >
> >
> >
> >
> >
> >
> >
> >
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] [***Posible SPAM***]2

[Farzaneh Farzadi]

Dear users

I'm a new user of SIESTA code (siesta-3.2 version). Please help me with the
following trouble:
 I need the Pdosxml executive file to draw .PDOS, but this executive file
is not created in pdosxml folder via "make" command and a screen appears
indicating the following error:

"Making sure that the xmlparser library is compiled...
(cd ../../Obj/xmlparser ; make "VPATH=../../Src/xmlparser")
make[1]: Entering directory
'/home/farzadi/pakage/siesta-3.2-pl-5/Obj/xmlparser'
make[1]: Nothing to be done for 'module'.
make[1]: Leaving directory
'/home/farzadi/pakage/siesta-3.2-pl-5/Obj/xmlparser'
f95  -c -g -O2  -I../../Obj/xmlparserm_pdos.f90
m_pdos.f90:13:4:
 use flib_sax
   1
Fatal Error: Cannot read module file ‘flib_sax.mod’ opened at (1), because
it was created by a different version of GNU Fortran
compilation terminated.
../../Obj/arch.make:66: recipe for target 'm_pdos.o' failed
make: *** [m_pdos.o] Error 1"

I would be really appreciated if anyone can help me with this problem.
Regards

Re: [SIESTA-L] [***Posible SPAM***]2

[Nick Papior]

Fatal Error: Cannot read module file ‘flib_sax.mod’ opened at (1),
because it was created by a different version of GNU Fortran
compilation terminated.

Do make clean...

2016-03-18 16:57 GMT+01:00 Farzaneh Farzadi :
> Dear users
>
> I'm a new user of SIESTA code (siesta-3.2 version). Please help me with the
> following trouble:
>  I need the Pdosxml executive file to draw .PDOS, but this executive file is
> not created in pdosxml folder via "make" command and a screen appears
> indicating the following error:
>
> "Making sure that the xmlparser library is compiled...
> (cd ../../Obj/xmlparser ; make "VPATH=../../Src/xmlparser")
> make[1]: Entering directory
> '/home/farzadi/pakage/siesta-3.2-pl-5/Obj/xmlparser'
> make[1]: Nothing to be done for 'module'.
> make[1]: Leaving directory
> '/home/farzadi/pakage/siesta-3.2-pl-5/Obj/xmlparser'
> f95  -c -g -O2  -I../../Obj/xmlparserm_pdos.f90
> m_pdos.f90:13:4:
>  use flib_sax
>1
> Fatal Error: Cannot read module file ‘flib_sax.mod’ opened at (1), because
> it was created by a different version of GNU Fortran
> compilation terminated.
> ../../Obj/arch.make:66: recipe for target 'm_pdos.o' failed
> make: *** [m_pdos.o] Error 1"
>
> I would be really appreciated if anyone can help me with this problem.
> Regards
>
>
>
>
>
>
>
>



-- 
Kind regards Nick

Re: [SIESTA-L] [***Posible SPAM***]2

[sauluck]

barnali,
send a ps or pdf fileof the band structure & name of compound.
s.auluck

> Thank you sir for your kind response. My system is a metallic one where
> the
> Fermi energy sifted towards conduction band due to doping. For details
> here
> I am attaching the band structure. Do you think should I include drude
> term? Kindly guide me to chose relaxation time for my system.
>
> I am waiting for your suggestion.
>
> Thanks in advance.
>
> Sincerely
> Barnali
>
>
> On Wed, Feb 17, 2016 at 6:02 PM,  wrote:
>
>> barnali,
>> drude term is to included only when a band/bands cut the fermi
>> energy...for
>> metals,semimetals..if you have an energy gap then you have only
>> interband contributions..no drde term.
>> s.auluck
>>
>> > Respected SIESTA users (Marty Blaber)
>> >
>> > I am calculating the optical properties of  a graphene like  2D sheet
>> > using
>> > SIESTA 3.2. The band structure confirms its metallic nature and  the
>> > *.EPSIMG (was generated after optical calculation) shows  W_p is
>> non-zero,
>> > i.e.  W_p =0.0013.  As I know that the  drude term is to be included
>> for
>> > metal, now my queries are -
>> > For calculating optical properties  using optical.f should I  include
>> > drude term?
>> >  Is it necessary to include drude term for my system? If it is
>> necessary,
>> > then how can I choose relaxation time?  I will be grateful if anyone
>> > guide
>> > me to choose relaxation time for graphene like 2D sheet? I am waiting
>> for
>> > any response.
>> >
>> > Thanks in advance.
>> >
>> > Sincerely
>> > Barnali Bhattacharya
>> > Ph.D. Student,
>> >  Assam University, Silchar, India
>> >
>>
>>
>> --
>> Prof. Sushil Auluck  Phone:+91-512-6797092/6148
>> Department of Physics  +91-512-6798177(Home)
>> Indian Institute of Technology   Cell :+91-9305548667
>> Kanpur 208016 (UP)   Fax  :+91-512-6790914
>> IndiaE-mail:saul...@iitk.ac.in
>>  ...:saul...@gmail.com
>> http://www.iitk.ac.in/phy/People/phy_facvis.html
>> http://www.iitk.ac.in/phy/New01/profile_SA.html
>> http://www.iitk.ac.in/phy/index.php/people/faculty
>>
>> http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
>> ...
>> ~
>>
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
http://www.iitk.ac.in/phy/index.php/people/faculty
http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
...
~

Re: [SIESTA-L] [***Posible SPAM***]2

[Barnali Bhattacharya]

Thank you sir for your kind response. My system is a metallic one where the
Fermi energy sifted towards conduction band due to doping. For details here
I am attaching the band structure. Do you think should I include drude
term? Kindly guide me to chose relaxation time for my system.

I am waiting for your suggestion.

Thanks in advance.

Sincerely
Barnali


On Wed, Feb 17, 2016 at 6:02 PM,  wrote:

> barnali,
> drude term is to included only when a band/bands cut the fermi energy...for
> metals,semimetals..if you have an energy gap then you have only
> interband contributions..no drde term.
> s.auluck
>
> > Respected SIESTA users (Marty Blaber)
> >
> > I am calculating the optical properties of  a graphene like  2D sheet
> > using
> > SIESTA 3.2. The band structure confirms its metallic nature and  the
> > *.EPSIMG (was generated after optical calculation) shows  W_p is
> non-zero,
> > i.e.  W_p =0.0013.  As I know that the  drude term is to be included for
> > metal, now my queries are -
> > For calculating optical properties  using optical.f should I  include
> > drude term?
> >  Is it necessary to include drude term for my system? If it is necessary,
> > then how can I choose relaxation time?  I will be grateful if anyone
> > guide
> > me to choose relaxation time for graphene like 2D sheet? I am waiting for
> > any response.
> >
> > Thanks in advance.
> >
> > Sincerely
> > Barnali Bhattacharya
> > Ph.D. Student,
> >  Assam University, Silchar, India
> >
>
>
> --
> Prof. Sushil Auluck  Phone:+91-512-6797092/6148
> Department of Physics  +91-512-6798177(Home)
> Indian Institute of Technology   Cell :+91-9305548667
> Kanpur 208016 (UP)   Fax  :+91-512-6790914
> IndiaE-mail:saul...@iitk.ac.in
>  ...:saul...@gmail.com
> http://www.iitk.ac.in/phy/People/phy_facvis.html
> http://www.iitk.ac.in/phy/New01/profile_SA.html
> http://www.iitk.ac.in/phy/index.php/people/faculty
>
> http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
> ...
> ~
>


2N_CHAIN
Description: Binary data

Re: [SIESTA-L] [***Posible SPAM***]2

[sauluck]

barnali,
drude term is to included only when a band/bands cut the fermi energy...for
metals,semimetals..if you have an energy gap then you have only
interband contributions..no drde term.
s.auluck

> Respected SIESTA users (Marty Blaber)
>
> I am calculating the optical properties of  a graphene like  2D sheet
> using
> SIESTA 3.2. The band structure confirms its metallic nature and  the
> *.EPSIMG (was generated after optical calculation) shows  W_p is non-zero,
> i.e.  W_p =0.0013.  As I know that the  drude term is to be included for
> metal, now my queries are -
> For calculating optical properties  using optical.f should I  include
> drude term?
>  Is it necessary to include drude term for my system? If it is necessary,
> then how can I choose relaxation time?  I will be grateful if anyone
> guide
> me to choose relaxation time for graphene like 2D sheet? I am waiting for
> any response.
>
> Thanks in advance.
>
> Sincerely
> Barnali Bhattacharya
> Ph.D. Student,
>  Assam University, Silchar, India
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
http://www.iitk.ac.in/phy/index.php/people/faculty
http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
...
~

[SIESTA-L] [***Posible SPAM***]2

[Barnali Bhattacharya]

Respected SIESTA users (Marty Blaber)

I am calculating the optical properties of  a graphene like  2D sheet using
SIESTA 3.2. The band structure confirms its metallic nature and  the
*.EPSIMG (was generated after optical calculation) shows  W_p is non-zero,
i.e.  W_p =0.0013.  As I know that the  drude term is to be included for
metal, now my queries are -
For calculating optical properties  using optical.f should I  include
drude term?
 Is it necessary to include drude term for my system? If it is necessary,
then how can I choose relaxation time?  I will be grateful if anyone  guide
me to choose relaxation time for graphene like 2D sheet? I am waiting for
any response.

Thanks in advance.

Sincerely
Barnali Bhattacharya
Ph.D. Student,
 Assam University, Silchar, India

[SIESTA-L] [***Posible SPAM***]FW: citation of SIESTA

[Ludwig , Stephan]



-Original message-
From: Ludwig, Stephan 
Sent: Monday 28th December 2015 18:54
To: siesta...@uam.es (siesta-l-requ...@uam.es) 
Subject: citation of SIESTA

 

Hello everybody,



is there a bibtex file prepered in order to cite the use of Siesta. I mean 
something like this for Quantum Espresso



@article{QE-2009,
    Author = {Paolo Giannozzi and Stefano Baroni and Nicola Bonini and Matteo 
Calandra and Roberto Car and Carlo Cavazzoni and Davide Ceresoli and Guido L 
Chiarotti and Matteo Cococcioni and Ismaila Dabo and Andrea {Dal Corso} and 
Stefano de Gironcoli and Stefano Fabris and Guido Fratesi and Ralph Gebauer and 
Uwe Gerstmann and Christos Gougoussis and Anton Kokalj and Michele Lazzeri and 
Layla Martin-Samos and Nicola Marzari and Francesco Mauri and Riccardo 
Mazzarello and Stefano Paolini and Alfredo Pasquarello and Lorenzo Paulatto and 
Carlo Sbraccia and Sandro Scandolo and Gabriele Sclauzero and Ari P Seitsonen 
and Alexander Smogunov and Paolo Umari and Renata M Wentzcovitch},
    Journal = {Journal of Physics: Condensed Matter},
    Number = {39},
    Pages = {395502 (19pp)},
    Title = {QUANTUM ESPRESSO: a modular and open-source software project for 
quantum simulations of materials},
    Url = {http://www.quantum-espresso.org  },
    Volume = {21},
    Year = {2009}}



If there is not such a file. Can someone please give me a guideline how to cite 
SIESTA?



Thanks and regards



Stephan

[SIESTA-L] [***Posible SPAM***]

[Eliya Asmani]

Dear all

I want to calculate the optical properties of monolayer graphene. My result
for the dielectric constan (epsilon_real and epsilon_imag ) in the
x-direction is correct but when direction is set the z-direction, the
result are incorrect.
I wonde if somebody of you can help me.
My fdf file is listed as follow:

SystemName  graphene
SystemLabel C
NumberOfAtoms   2
NumberOfSpecies 1

%block ChemicalSpeciesLabel
 1  6  C  # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

LatticeConstant 1.0   Ang

%block LatticeParameters
   2.42 2.42  10.0   90.  90.  120. # (could be 120. instead of 60.)
%endblock LatticeParameters

AtomicCoordinatesFormat Fractional

%block AtomicCoordinatesAndAtomicSpecies
 0. 0. 0. 1
 0. 0. 0. 1
%endblock AtomicCoordinatesAndAtomicSpecies

%block kgrid_Monkhorst_Pack
 80000.5
  0   8000.5
%endblock kgrid_Monkhorst_Pack

DM.Tolerance 10-6
DM.Require.Energy.Convergence  true
DM.Energy.Tolerance  10-6 eV
DM.Require.Harris.Convergence  true
DM.Harris.Tolerance  10-6  eV
MeshCutoff400 Ry
PAO.EnergyShift 0.01 Ry

XC.functional  GGA
XC.authors PBE

OpticalCalculation  true

Optical.EnergyMinimum   0.0  eV
Optical.EnergyMaximum   40.0 eV

%block Optical.Vector
0.0 0.0 1.0
%endblock Optical.Vector

Optical.PolarizationType  polarized

Optical.Broaden   0.1 eV

%block  Optical.Mesh
 150 150 50
%endblock  Optical.Mesh

[SIESTA-L] [***Posible SPAM***]

[Soumaia Djaadi]

Hi all, I want  calculate the optics properties of the clusters atomic but the 
results illogical for example the refrax-index in area 0.98-1.001. Do we have 
to change DFT to TDDFT and How to use TDDFT in siesta 3 cod?

[SIESTA-L] [***Posible SPAM***]

[Riya Rogers]

Hello everyone

Re: [SIESTA-L] [***Posible SPAM***]

[Younas Khan]

Hello and welcome to siesta community.


On Fri, Oct 2, 2015 at 8:51 PM, Riya Rogers  wrote:

> Hello everyone
>

Re: [SIESTA-L] [***Posible SPAM***]Fortran runtime error

[Nick Papior]

Please try the latest trunk version available and see if it helps. If not
report the error message that it returned.

2015-09-01 7:26 GMT+02:00 Saeed Nasiri :

> Dear users
>
> I have a problem when I run the vibrator and the familiar "Fortran runtime
> error" caused the code to stop. I have seen many topics about this error
> and all of them form GCC site and I can't find a solution. Could anyone
> help me?
>
> Your sincerely
> Nasiri
>
> vibrator < coronene36.fdf
> redata: System Name  =
> coronene36
>
> redata: System Label =
> coronene36
>
> Number of Atoms  =36
> Lattice Constant=   37.79454  Bohr
> Lattice vectors (in units of Lattice Constant) =
>1.0   0.0   0.0
>0.0   1.0   0.0
>0.0   0.0   1.0
> Lattice vectors (in Bohr) =
>   37.79454   0.0   0.0
>0.0  37.79454   0.0
>0.0   0.0  37.79454
> recoor: Atomic-coordinates input format  = Cartesian coordinates
> recoor:(in Angstroms)
> recoor: Atomic coordinates (Bohr) and species
> recoor:1 2.37161   6.72365   0.0  1
> recoor:2 0.0   5.41218   0.0  1
> recoor:3 0.0   2.71176   0.0  1
> recoor:4 2.34893   1.35682   0.0  1
> recoor:5 4.68652   2.70609   0.0  1
> recoor:6 4.63739   5.41596   0.0  1
> recoor:7-2.34893   1.35682   0.0  1
> recoor:8 2.34893  -1.35682   0.0  1
> recoor:9 0.0  -2.71176   0.0  1
> recoor:   10-2.34893  -1.35682   0.0  1
> recoor:   11 0.0  -5.41218   0.0  1
> recoor:   12 2.37161  -6.72365   0.0  1
> recoor:   13 4.63739  -5.41596   0.0  1
> recoor:   14 4.68652  -2.70609   0.0  1
> recoor:   15 7.00900  -1.30769   0.0  1
> recoor:   16 7.00900   1.30769   0.0  1
> recoor:   17 8.78345   2.34326   0.0  2
> recoor:   18 8.78345  -2.34326   0.0  2
> recoor:   19 2.36216   8.77967   0.0  2
> recoor:   20 6.42129   6.43641   0.0  2
> recoor:   21 2.36216  -8.77967   0.0  2
> recoor:   22 6.42129  -6.43641   0.0  2
> recoor:   23-2.37161   6.72365   0.0  1
> recoor:   24-4.63739   5.41596   0.0  1
> recoor:   25-4.68652   2.70609   0.0  1
> recoor:   26-2.36216   8.77967   0.0  2
> recoor:   27-6.42129   6.43641   0.0  2
> recoor:   28-7.00900   1.30769   0.0  1
> recoor:   29-7.00900  -1.30769   0.0  1
> recoor:   30-4.68652  -2.70609   0.0  1
> recoor:   31-8.78345   2.34326   0.0  2
> recoor:   32-8.78345  -2.34326   0.0  2
> recoor:   33-2.37161  -6.72365   0.0  1
> recoor:   34-2.36216  -8.77967   0.0  2
> recoor:   35-4.63739  -5.41596   0.0  1
> recoor:   36-6.42129  -6.43641   0.0  2
> lxmax= 0
> lymax= 0
> lzmax= 0
> Number of unit cells in Supercell  = 1
> Eigenvectors =   True
> Computing Eigenvalues and Eigenvectors
>   eigenvalue #   1  omega=  -168.85753666525625
>   eigenvalue #   2  omega=  -133.60573713877807
>   eigenvalue #   3  omega=  -121.54941729933871
>   eigenvalue #   4  omega=  -110.90174013078901
>   eigenvalue #   5  omega=  -99.749277919748764
>   eigenvalue #   6  omega=  -90.083077076681178
>   eigenvalue #   7  omega=  -58.694544266527870
>   eigenvalue #   8  omega=  -52.626623303401814
>   eigenvalue #   9  omega=  -45.376121225776892
>   eigenvalue #  10  omega=  -43.736373657465357
>   eigenvalue #  11  omega=  -42.648817688569459
>   eigenvalue #  12  omega=  -38.839596864377356
>   eigenvalue #  13  omega= -0.10273295354208219
>   eigenvalue #  14  omega=  -8.7029675504071147E-002
>   eigenvalue #  15  omega=  -5.9354628384510749E-002
>   eigenvalue #  16  omega=   30.853769190014759
>   eigenvalue #  17  omega=   70.341957600505381
>   eigenvalue #  18  omega=   70.559152018112869
>   eigenvalue #  19  omega=   72.404584738159954
>   eigenvalue #  20  omega=   76.648478571924883
>   eigenvalue #  21  omega=   90.837639896855151
>   eigenvalue #  22  omega=   94.264302495164301
>   eigenvalue #  23  omega=   104.10894100039582
>   eigenvalue #  24  omega=   106.48747834610091
>   eigenvalue #  25  omega=   118.50202515332684
>   eigenvalue #  26  omega=   121.79062186039529
>   eigenvalue #  27  omega=   126.99926407184333
>   eigenvalue #  28  omega=   136.04423221052491
>   eigenvalue #  29  omega=   139.66302675242721
>   eigenvalue #  30  omega=   152.31638420999138
>   eigenvalue #  31  omega=   155.61259095878492
>   eigenvalue #  

[SIESTA-L] [***Posible SPAM***]Fortran runtime error

[Saeed Nasiri]

Dear users

I have a problem when I run the vibrator and the familiar "Fortran runtime
error" caused the code to stop. I have seen many topics about this error
and all of them form GCC site and I can't find a solution. Could anyone
help me?

Your sincerely
Nasiri

vibrator < coronene36.fdf
redata: System Name  =
coronene36

redata: System Label =
coronene36

Number of Atoms  =36
Lattice Constant=   37.79454  Bohr
Lattice vectors (in units of Lattice Constant) =
   1.0   0.0   0.0
   0.0   1.0   0.0
   0.0   0.0   1.0
Lattice vectors (in Bohr) =
  37.79454   0.0   0.0
   0.0  37.79454   0.0
   0.0   0.0  37.79454
recoor: Atomic-coordinates input format  = Cartesian coordinates
recoor:(in Angstroms)
recoor: Atomic coordinates (Bohr) and species
recoor:1 2.37161   6.72365   0.0  1
recoor:2 0.0   5.41218   0.0  1
recoor:3 0.0   2.71176   0.0  1
recoor:4 2.34893   1.35682   0.0  1
recoor:5 4.68652   2.70609   0.0  1
recoor:6 4.63739   5.41596   0.0  1
recoor:7-2.34893   1.35682   0.0  1
recoor:8 2.34893  -1.35682   0.0  1
recoor:9 0.0  -2.71176   0.0  1
recoor:   10-2.34893  -1.35682   0.0  1
recoor:   11 0.0  -5.41218   0.0  1
recoor:   12 2.37161  -6.72365   0.0  1
recoor:   13 4.63739  -5.41596   0.0  1
recoor:   14 4.68652  -2.70609   0.0  1
recoor:   15 7.00900  -1.30769   0.0  1
recoor:   16 7.00900   1.30769   0.0  1
recoor:   17 8.78345   2.34326   0.0  2
recoor:   18 8.78345  -2.34326   0.0  2
recoor:   19 2.36216   8.77967   0.0  2
recoor:   20 6.42129   6.43641   0.0  2
recoor:   21 2.36216  -8.77967   0.0  2
recoor:   22 6.42129  -6.43641   0.0  2
recoor:   23-2.37161   6.72365   0.0  1
recoor:   24-4.63739   5.41596   0.0  1
recoor:   25-4.68652   2.70609   0.0  1
recoor:   26-2.36216   8.77967   0.0  2
recoor:   27-6.42129   6.43641   0.0  2
recoor:   28-7.00900   1.30769   0.0  1
recoor:   29-7.00900  -1.30769   0.0  1
recoor:   30-4.68652  -2.70609   0.0  1
recoor:   31-8.78345   2.34326   0.0  2
recoor:   32-8.78345  -2.34326   0.0  2
recoor:   33-2.37161  -6.72365   0.0  1
recoor:   34-2.36216  -8.77967   0.0  2
recoor:   35-4.63739  -5.41596   0.0  1
recoor:   36-6.42129  -6.43641   0.0  2
lxmax= 0
lymax= 0
lzmax= 0
Number of unit cells in Supercell  = 1
Eigenvectors =   True
Computing Eigenvalues and Eigenvectors
  eigenvalue #   1  omega=  -168.85753666525625
  eigenvalue #   2  omega=  -133.60573713877807
  eigenvalue #   3  omega=  -121.54941729933871
  eigenvalue #   4  omega=  -110.90174013078901
  eigenvalue #   5  omega=  -99.749277919748764
  eigenvalue #   6  omega=  -90.083077076681178
  eigenvalue #   7  omega=  -58.694544266527870
  eigenvalue #   8  omega=  -52.626623303401814
  eigenvalue #   9  omega=  -45.376121225776892
  eigenvalue #  10  omega=  -43.736373657465357
  eigenvalue #  11  omega=  -42.648817688569459
  eigenvalue #  12  omega=  -38.839596864377356
  eigenvalue #  13  omega= -0.10273295354208219
  eigenvalue #  14  omega=  -8.7029675504071147E-002
  eigenvalue #  15  omega=  -5.9354628384510749E-002
  eigenvalue #  16  omega=   30.853769190014759
  eigenvalue #  17  omega=   70.341957600505381
  eigenvalue #  18  omega=   70.559152018112869
  eigenvalue #  19  omega=   72.404584738159954
  eigenvalue #  20  omega=   76.648478571924883
  eigenvalue #  21  omega=   90.837639896855151
  eigenvalue #  22  omega=   94.264302495164301
  eigenvalue #  23  omega=   104.10894100039582
  eigenvalue #  24  omega=   106.48747834610091
  eigenvalue #  25  omega=   118.50202515332684
  eigenvalue #  26  omega=   121.79062186039529
  eigenvalue #  27  omega=   126.99926407184333
  eigenvalue #  28  omega=   136.04423221052491
  eigenvalue #  29  omega=   139.66302675242721
  eigenvalue #  30  omega=   152.31638420999138
  eigenvalue #  31  omega=   155.61259095878492
  eigenvalue #  32  omega=   195.35098263626890
  eigenvalue #  33  omega=   206.40255867987719
  eigenvalue #  34  omega=   209.01692338659882
  eigenvalue #  35  omega=   219.45454874057535
  eigenvalue #  36  omega=   228.51254971263401
  eigenvalue #  37  omega=   229.44144017812971
  eigenvalue #  38  omega=   262.09487191250400
  eigenvalue #   

[SIESTA-L] [***Posible SPAM***]

[Barnali Bhattacharya]

Dear Sir/Madam,



   When I am trying to run the siesta parallel, I got the
following error-



………

New_DM. Step: 1

Initializing Density Matrix...



InitMesh: MESH =60 x60 x   216 =  777600

InitMesh: Mesh cutoff (required, used) =   525.000   548.583 Ry



* Maximum dynamic memory allocated =21 MB



stepf: Fermi-Dirac step function

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

ERROR STOP from Node:   12

Fermid: Iteration has not converged.

ERROR STOP from Node:   28

Fermid: Iteration has not converged.

ERROR STOP from Node:   30

Fermid: Iteration has not converged.

ERROR STOP from Node:   27

ERROR STOP from Node:   19

Fermid: Iteration has not converged.

ERROR STOP from Node:   35

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

ERROR STOP from Node:   55

Fermid: Iteration has not converged.

Fermid: Iteration has not converged.

ERROR STOP from Node:   56



I have taken different input file (which already run successfully in
another machine), but all the time same error appeared. Now my questions
are-

Why this error appeared? Is there anything wrong in my installation? Do I
miss anything?

Could anyone please guide me to fix this problem?  Here I have attached the
output file for details information.

Thanking you.



Sincerely



Barnali Bhattacharya

Ph.D student, Physics Department

Assam University, Silchar.


GRAPHENE_22.out
Description: Binary data

Re: [SIESTA-L] [***Posible SPAM***]

[Nick Papior]

Do not use that many processors for so few atoms. This may be the reason.
A good advice is to use no more than the number of atoms in your system.

However, in your case you use a lot of k-points.
Then look up the fdf flag Diag.ParallelOverK.


2015-08-26 15:13 GMT+02:00 Barnali Bhattacharya barnalidgbh...@gmail.com:

 Dear Sir/Madam,



When I am trying to run the siesta parallel, I got the
 following error-



 ………

 New_DM. Step: 1

 Initializing Density Matrix...



 InitMesh: MESH =60 x60 x   216 =  777600

 InitMesh: Mesh cutoff (required, used) =   525.000   548.583 Ry



 * Maximum dynamic memory allocated =21 MB



 stepf: Fermi-Dirac step function

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   12

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   28

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   30

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   27

 ERROR STOP from Node:   19

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   35

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   55

 Fermid: Iteration has not converged.

 Fermid: Iteration has not converged.

 ERROR STOP from Node:   56

 

 I have taken different input file (which already run successfully in
 another machine), but all the time same error appeared. Now my questions
 are-

 Why this error appeared? Is there anything wrong in my installation? Do I
 miss anything?

 Could anyone please guide me to fix this problem?  Here I have attached
 the output file for details information.

 Thanking you.



 Sincerely



 Barnali Bhattacharya

 Ph.D student, Physics Department

 Assam University, Silchar.






-- 
Kind regards Nick

[SIESTA-L] [***Posible SPAM***]

[Altaf Ur Rahman]

Hello. I have question concerning with band structure calculation of
Topological Insulator , can it be done when when we take   *SOC .true.*
   using siesta or not ?
Thanks in advance

Re: [SIESTA-L] [***Posible SPAM***]

[wososac]

Thanks Roberto,


I have problem with the Mesh cutoff convergence

 1_300_Ry/RUN.out:siesta: Total =   -2372.317138
 2_320_Ry/RUN.out:siesta: Total =   -2372.317138
 3_340_Ry/RUN.out:siesta: Total =   -2372.317138
 4_360_Ry/RUN.out:siesta: Total =   -2372.317138
 5_380_Ry/RUN.out:siesta: Total =   -2372.317356
 6_400_Ry/RUN.out:siesta: Total =   -2372.214550
 7_420_Ry/RUN.out:siesta: Total =   -2372.213248
 8_440_Ry/RUN.out:siesta: Total =   -2372.213248
 9_460_Ry/RUN.out:siesta: Total =   -2372.213010
10_480_Ry/RUN.out:siesta: Total =   -2372.213010
11_500_Ry/RUN.out:siesta: Total =   -2372.213010
12_520_Ry/RUN.out:siesta: Total =   -2372.316896
13_540_Ry/RUN.out:siesta: Total =   -2372.542573
14_560_Ry/RUN.out:siesta: Total =   -2372.316896
15_580_Ry/RUN.out:siesta: Total =   -2372.740691
16_600_Ry/RUN.out:siesta: Total =   -2372.740691


Do you have any advice for me about these systems?


 Hi,

 I think you are missunderstanding the distance axis of the
 pseudopotential components: r=2 (a.u.) means 2 Bohr, which is
 about 1 Angstrom.

 Regards,

 Roberto


 On 06/22/2015 05:17 PM, woso...@df.ufpe.br wrote:
 Dear users

 My name is William Sosa the purpose of this email is
 about of some problems with SIESTA, specifically i am studing the spin
 electronic transport in 1D systems, I have a problem with the
 pseudopotential GGA for short interatomic distances (about 2 Angstroms)
 in
 the Ni-Ni and Fe-Fe bonds since the pseudopotentials in the database
 are
 for greater distances, Are there some pseudopotential for these
 distances?

 Also I want know if is possible fix the spin in the electrodes for
 TranSIESTA calculations?

 Thanks you for your help.

 Regards,


 William Sosa.
|-|

Re: [SIESTA-L] [***Posible SPAM***]

[RCP]

Hello William,

Your output says nothing to me, in the first place, how do
you know you're having a problem?.

Mesh cutoff refers to the grid size for numerical integrations
in real space (different thing from plane wave codes). Values
in the range 300 to 500 Ry should be pretty fine. The larger the
finer the grid.
But most important is DM.Tolerance parameter; this is what you
mostly monitor for convergence. 1.d-3 might be ok, better if 1.d-4.
And do not forget MP grid in k space, metalls need the equivalent
of some few hundred k-points per primitive cell.

Good luck,

Roberto


On 06/23/2015 03:46 PM, woso...@df.ufpe.br wrote:

Thanks Roberto,


I have problem with the Mesh cutoff convergence

  1_300_Ry/RUN.out:siesta: Total =   -2372.317138
  2_320_Ry/RUN.out:siesta: Total =   -2372.317138
  3_340_Ry/RUN.out:siesta: Total =   -2372.317138
  4_360_Ry/RUN.out:siesta: Total =   -2372.317138
  5_380_Ry/RUN.out:siesta: Total =   -2372.317356
  6_400_Ry/RUN.out:siesta: Total =   -2372.214550
  7_420_Ry/RUN.out:siesta: Total =   -2372.213248
  8_440_Ry/RUN.out:siesta: Total =   -2372.213248
  9_460_Ry/RUN.out:siesta: Total =   -2372.213010
10_480_Ry/RUN.out:siesta: Total =   -2372.213010
11_500_Ry/RUN.out:siesta: Total =   -2372.213010
12_520_Ry/RUN.out:siesta: Total =   -2372.316896
13_540_Ry/RUN.out:siesta: Total =   -2372.542573
14_560_Ry/RUN.out:siesta: Total =   -2372.316896
15_580_Ry/RUN.out:siesta: Total =   -2372.740691
16_600_Ry/RUN.out:siesta: Total =   -2372.740691


Do you have any advice for me about these systems?

Re: [SIESTA-L] [***Posible SPAM***]

[RCP]

Hi,

I think you are missunderstanding the distance axis of the
pseudopotential components: r=2 (a.u.) means 2 Bohr, which is
about 1 Angstrom.

Regards,

Roberto


On 06/22/2015 05:17 PM, woso...@df.ufpe.br wrote:

Dear users


My name is William Sosa the purpose of this email is
about of some problems with SIESTA, specifically i am studing the spin
electronic transport in 1D systems, I have a problem with the
pseudopotential GGA for short interatomic distances (about 2 Angstroms) in
the Ni-Ni and Fe-Fe bonds since the pseudopotentials in the database are
for greater distances, Are there some pseudopotential for these distances?

Also I want know if is possible fix the spin in the electrodes for
TranSIESTA calculations?

Thanks you for your help.

Regards,




William Sosa.

|-|

[SIESTA-L] [***Posible SPAM***]

[wososac]

Dear users

 My name is William Sosa the purpose of this email is
 about of some problems with SIESTA, specifically i am studing the spin
 electronic transport in 1D systems, I have a problem with the
 pseudopotential GGA for short interatomic distances (about 2 Angstroms) in
 the Ni-Ni and Fe-Fe bonds since the pseudopotentials in the database are
 for greater distances, Are there some pseudopotential for these distances?

 Also I want know if is possible fix the spin in the electrodes for
 TranSIESTA calculations?

 Thanks you for your help.

 Regards,


 William Sosa.

[SIESTA-L] [***Posible SPAM***]GGA Pseudopotential for Tungsten

[Seyed Mohammad Tabatabaei]

Dear all,

I would be really grateful if anyone can a share a GGA pseudo potential for
Tungsten atom with me. I am also in need of the input file for the ATOM
program.

Bests,
Mohammad,

Re: [SIESTA-L] [***Posible SPAM***]

[Mourad Boutahir]

I would calculate the tensor of polarisabity not raman spectroscopy ?
Le 27 févr. 2015 06:26, Suman Chowdhury sumanchowdhur...@gmail.com a
écrit :

 As far as I am concern it is not possible to calculate raman spectroscopy
 by using siesta. You can calculate other DFT code such as quantum espresso
 or Gaussian for this.

 On Thu, Feb 26, 2015 at 9:51 PM, Mourad Boutahir 
 mourad.bouta...@gmail.com wrote:

 helo,
 i m phD in morocco i start to use the code siesta for dynamic
 calculations i would calculate the raman spectroscopy of some structures.
 so please if it was possible to indicate me how i can calculate the
 raman polarisabity model using the code siesta.

 best regards

 --

 ---
 *Mr. Mourad BOUTAHIR* ;
 Doctorant à la Faculté des sciences MEKNES ;
 Laboratoire d'Etude des Matériaux Avancés et Applications (LEM2A)
 Université Moulay Ismail
 GSM : +212662770697;
 E-mail : *mourad.bouta...@gmail.com mourad.bouta...@gmail.com**
 ait_ta...@yahoo.fr;*

 
 -




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*

Re: [SIESTA-L] [***Posible SPAM***]

[Suman Chowdhury]

As far as I am concern it is not possible to calculate raman spectroscopy
by using siesta. You can calculate other DFT code such as quantum espresso
or Gaussian for this.

On Thu, Feb 26, 2015 at 9:51 PM, Mourad Boutahir mourad.bouta...@gmail.com
wrote:

 helo,
 i m phD in morocco i start to use the code siesta for dynamic calculations
 i would calculate the raman spectroscopy of some structures.
 so please if it was possible to indicate me how i can calculate the  raman
 polarisabity model using the code siesta.

 best regards

 --

 ---
 *Mr. Mourad BOUTAHIR* ;
 Doctorant à la Faculté des sciences MEKNES ;
 Laboratoire d'Etude des Matériaux Avancés et Applications (LEM2A)
 Université Moulay Ismail
 GSM : +212662770697;
 E-mail : *mourad.bouta...@gmail.com mourad.bouta...@gmail.com**
 ait_ta...@yahoo.fr;*

 
 -




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] [***Posible SPAM***]

[Mourad Boutahir]

helo,
i m phD in morocco i start to use the code siesta for dynamic calculations
i would calculate the raman spectroscopy of some structures.
so please if it was possible to indicate me how i can calculate the  raman
polarisabity model using the code siesta.

best regards

-- 
---
*Mr. Mourad BOUTAHIR* ;
Doctorant à la Faculté des sciences MEKNES ;
Laboratoire d'Etude des Matériaux Avancés et Applications (LEM2A)
Université Moulay Ismail
GSM : +212662770697;
E-mail : *mourad.bouta...@gmail.com mourad.bouta...@gmail.com**
ait_ta...@yahoo.fr;*

-

[SIESTA-L] [***Posible SPAM***]

[Shiba Subedi]

-- 
Your Sincerely
Shiba Subedi
Central Department of Physics, Tribhuvan University
Kathmandu, Nepal

[SIESTA-L] [***Posible SPAM***][SOLVED] Problem with reproducing Vanadium lattice constant in a paper

[Sherif Tawfik]

I found that there is actually nothing wrong with the pseudo provided in
the ABINIT database; it gives a good estimate for the lattice constant
(about 3.06 Ang).

Sherif

[SIESTA-L] [***Posible SPAM***]

[Seyed Mohammad Tabatabaei]

Dear all siesta users,

Apparently, the latest trunk version of siesta takes care of vdW
forces. Does anyone know how vdW should be included in the
calculations? There is a flag named XC.authors
and the manual says that it should be set to DRSLL. Is it OK to use
the existing pseudos when including vdW interactions? I would be
really grateful if you share with me your experience on this.
Moreover, is it OK to use the trunk version results for publication?
Are they credible?

Best wishes,
Mohammad,
University of Tehran,

[SIESTA-L] [***Posible SPAM***]

[Manjeet Bhatia]

Dear Siesta Users,

I have problem in optimizing the Porphyrin structure (78 atoms). In my
output file I got total forces and pressure as follows:

Tot: 0.001825-0.0280930.005261
Pressure: 0.03   -0.02   kbar


and unrelaxed coordinates.  Does it mean that my relaxation is incomplete?
I look forward to your reply.

Thanks.

Re: [SIESTA-L] [***Posible SPAM***]

[Sonu Kumar]

Please, make proper Heading of your mail.




On Mon, Sep 8, 2014 at 3:13 PM, Manjeet Bhatia manjeetbhati...@gmail.com
wrote:

 Dear Siesta Users,

 I am doing spin polarized calculations for Pt. I have used GGA
 pseudopotential provided by siesta but I am getting valance
 configuration 5d10 in my output file closed shell.



 initatom: Reading input for the pseudopotentials and atomic orbitals
 --
  Species number:1  Label: Pt_GGA Atomic number:  78
 Ground state valence configuration:   5d10
 Reading pseudopotential information in formatted form from Pt_GGA.psf

 and

 Initializing Density Matrix...
 initdm: WARNING: atom  1 has a closed-shell and cannot be polarized


 Could you please let me know what parameters I have to change to get
 configuration 5d9 6s1 for spin calculation?

 Thanks.