Re: [SIESTA-L] Help regarding pdosxml and Eig2dos utility

[Mostafa Shabani]

Dear siesta user
Inside the pdosxml folder, there is a file "m_orbital_chooser.f90" and you
should edit it based on your interest atoms and orbitals. The line you
should edit it is
wantit = (( orbid%species == "Fe" ) .and. ( orbid%n == 3 ) .and. (orbid%l
== 2 ))this line extract  (n=3, l=2 , Fe)   3d orbital for Fe
atoms datas from pdos output file.
after you edit this file type make in terminal . and by this command
pdosxml > filename.txt you can obtain the results you want and you can plot
it easily by xmgrace.

On Tue, Nov 21, 2017 at 6:35 AM, BISWAJIT BALL 
wrote:

> Dear Siesta Users,
>
>
>   I am trying to plot pdos using pdosxml and Eig2dos utility. While
> using pdosxml I have systemlabel.pdos file and after running job by using
> command ./pdosxml systemlabel.pdos>x.dat I am getting a x.dat file.
> But the plotting gives only a straight line i.e in the x.dat file out
> of three columns two columns are zero although my system is not spin
> polarised. I want to calculate the individual atoms pdos and understand the
> meaning of each line in m_orbitalchooser.f90 file.
>
>  I have the systemlabel.EIG file and after running job by using
> command Eig2dos -s 0.2 -n 400 -m -15 -M 15 system label, i am getting an
> outputfile but the plotting gives only total pdos.
>   I want to plot individual atoms pdos by using Eig2dos and pdosxml
> utility. So, kindly help me in this regard.
>
>  With best regards
>

Re: [SIESTA-L] Defining periodic structure

[Mostafa Shabani]

Dear HarsH

A1- For making a structure you need lattice vectors and atomic position
coordinates of your unit cell structure to put in your input fdf file that
you can find in the papers or some material structure databases.

A2- You can check it by 3D structure visualization programs like VESTA
or *XCrySDen
*to see whether the structure is periodic or not

A3- After optimize some crucial parameter values  like (k-point and
Mesh-Cutoff) by set MD.MaxForceTol in your input fdf file you can optimize
your structure by MD (Molecular Dynamic) procedure.

Best regards,

)

On Tue, Nov 14, 2017 at 3:03 AM, Harsh Shah  wrote:

> 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

[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" <mostafa.nanophys...@gmail.com>
wrote:

> You should change the input fdf parameters based on new version.
>
> On Oct 23, 2017 18:00, "Farzaneh Farzadi" <f.farz...@gmail.com> 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*
>

[SIESTA-L] Transistors Key Parameters

[Mostafa Shabani]

Dear siesta user,
I have same questions about some transistors key parameters: (ON/OFF ratio,
transconductance, mobility, subthreshold swing)
I want to know how we can calculate this parameters? Is it possible to
calculate them with siesta/transiesta package?

Best regards

Re: [SIESTA-L] mobility, effective mass etc..

[Mostafa Shabani]

Dear siesta user,
I have same questions about some transistors key parameters: (ON/OFF ratio,
transconductance, mobility, subthreshold swing)
I want to know how we can calculate this parameters? Is it possible to
calculate them with siesta/transiesta package?

Best regards



On Sun, Oct 2, 2016 at 3:52 PM, Suman Chowdhury 
wrote:

> Dear SIESTA use,
> Does anyone know how to calculate effective mass, mobility, thermal and
> electrical conductivity, Seebeck coefficient through siesta simulation???
>
> --
>
>
>
> *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
> 79, West Bengal, India.*
> * Ph no-+91-9830512232*
>
>

Re: [SIESTA-L] Parallel compile and run

[Mostafa Shabani]

m_shabani1...@yahoo.com
On Jul 8, 2016 11:09 PM, "Arthur France-Lanord" 
wrote:

> Hi Mahmood,
>
> Another possibility, if you are managing that rocks cluster, would be to
> propagate packages installed on the head node to the slave nodes. Basically
> you’d have to edit a new xml config file, and build a new rocks distro.
>
> See eg.
> http://www.rocksclusters.org/roll-documentation/base/5.4/customization-adding-packages.html
>
> arthur
>
> On 08 Jul 2016, at 17:44, Mahmood Naderan  wrote:
>
> Hi again,
> There are some problems with the linking the libraries for parallel
> execution. The system is based on ROCKS and if an MPI jobs is going to be
> run on the compute nodes, all libraries should be available on the nodes.
> Anyway...
>
> As another try, I am rebuilding siesta parallel by downloading the source
> codes of the dependent libraries and install them on the NFS folder which
> is shared between nodes (the previous approach uses the package manager of
> the head node; hence nodes are not aware of that libraries).
>
> Please correct the following if I am wrong.
>
> Siesta needs the following libraries for a parallel run:
>   OpenMPI
>   LAPACK
>   BLACS
>   BLAS
>   SCALAPACK
>
> I have installed OpenMPI from source and it is fine. It seems that some of
> the above mentioned libraries are merged into others. For example,
> according to the release note of scalapack-2.0.0:
>
>   The BLACS is now part of ScaLAPACK, and is compiled into the
> ScaLAPACK library.  It is no longer necessary to link against BLACS
> libraries.
>
> After building Scalapack, I see libscalapack.a.
>
> Next, I downloaded LAPACK-3.6.1 and built it. The following libraries are
> built
>
>liblapack.a
>librefblas.a
>libtmglib.a
>
>
> So, I think everything that I need are present.
>
> Now, consider the following section of arch.make of siesta
>
> #BLAS_LIBS=-lcblas -lf77blas -latlas
> BLAS_LIBS=libblas.a
> LAPACK_LIBS=dc_lapack.a liblapack.a
> BLACS_LIBS=
> #BLACS_LIBS=-lblacsCinit -lblacsF77init -lblacs
> SCALAPACK_LIBS=-lscalapack
> # Tricky business ...
> NETCDF_INCFLAGS= -I/usr/include
> NETCDF_LIBS= -lnetcdf -lnetcdff
> #NETCDF_INTERFACE=libnetcdf_f90.a
> ​​
> LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
> $(NETCDF_LIBS)
>
>
> ​As I borrowed From Robert (RCP).
>
> I have to change those line, but I am not sure what to do. Here is my
> suggestion
>
> LAPACK_LIBS=liblapack.a librefblas.a libtmglib.a
> SCALAPACK_LIBS=libscalapack.a
> NETCDF_INCFLAGS= -I/usr/include
> NETCDF_LIBS= -lnetcdf -lnetcdff
> ​LIBS=$(SCALAPACK_LIBS) $(LAPACK_LIBS) $(NETCDF_LIBS)
>
> ​
> ​Any idea?​
>
>
> Regards,
> Mahmood
>
>
>

[SIESTA-L] constrain moves

[Mostafa Shabani]

Dear siesta users

For 20 atoms in unit cell we want to constrain all atoms moves in all
directions except for atoms number 11 and 16 that are fixes just in x and y
directions and are free to move in z direction.

W use this block GeometryConstraints in fdf input file


%block GeometryConstraints

position from -1 to -10
position from -12 to -15
position from -17 to -20
center 11 16 1.0  0.0  0.0
center 11 16 0.0  1.0  0.0

%endblock GeometryConstraints

is it true?


*Thanks in advance*

Re: [SIESTA-L] Relativistic Pseudo Potentials for MoS2

[Mostafa Shabani]

Dear Mohammad
As I know siesta doesn't employ relativistic pseudo potential. You can use
openMX pseudo potential.
در تاریخ 4 مهٔ 2015 19:58، Seyed Mohammad Tabatabaei smt...@gmail.com
نوشت:

 Dear all,

 I would be really grateful if anyone can provide me with the relativistic
 pseudo potential files for Mo and S that give a direct band gap for
 monolayer MoS2. The input files for the ATOM program are also deeply
 appreciated.

 Bests,
 Mohammad,

Re: [SIESTA-L] one question

[Mostafa Shabani]

I think you have to change split_norm  paramater in your fdf file. its
value is between 0 and 1. it determine how localize is your second zeta


On Sun, Jun 29, 2014 at 2:28 PM, Salami nadiasala...@gmail.com wrote:

  Dear Siesta users



 I want to relax the armchair MoS2(10), but after siesta running, I have
 faced to this error. I have took Mo.psf from Siesta web page. Should I
 build Mo.psf file?

  I would be really thankful for your comments and helps.

 Thanks in advance,

 Kind Regards.

 Nadia Salami







 atom: Called for Mo(Z =  42)



 read_vps: Pseudopotential generation method:

 read_vps: ATM3  Troullier-Martins

 Total valence charge:6.0



 read_vps: Pseudopotential includes a core correction:

 read_vps: Pseudo-core for xc-correction



 xc_check: Exchange-correlation functional:

 xc_check: GGA Perdew, Burke  Ernzerhof 1996

 V l=0 = -2*Zval/r beyond r=  3.3612

 V l=1 = -2*Zval/r beyond r=  3.3612

 V l=2 = -2*Zval/r beyond r=  3.3612

 V l=3 = -2*Zval/r beyond r=  3.3612

 All V_l potentials equal beyond r=  2.8216

 This should be close to max(r_c) in ps generation

 All pots = -2*Zval/r beyond r=  3.3612



 VLOCAL1: 99.0% of the norm of Vloc inside  5.452 Ry

 VLOCAL1: 99.9% of the norm of Vloc inside 12.426 Ry

 atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge3.36125

 atom: Maximum radius for r*vlocal+2*Zval:2.96629

 GHOST: No ghost state for L =  0

 GHOST: No ghost state for L =  1

 GHOST: No ghost state for L =  2

 GHOST: No ghost state for L =  3



 KBgen: Kleinman-Bylander projectors:

l= 0   rc=  3.761488   el= -0.278904   Ekb=  2.810542   kbcos=  0.286707

l= 1   rc=  3.856712   el= -0.075735   Ekb=  1.630125   kbcos=  0.263456

l= 2   rc=  3.403530   el= -0.293317   Ekb= -4.604863   kbcos= -0.604078

l= 3   rc=  4.004087   el=  0.003037   Ekb= -2.640656   kbcos= -0.020140



 KBgen: Total number of  Kleinman-Bylander projectors:   16

 atom:
 -



 atom: SANKEY-TYPE ORBITALS:

 atom: Selected multiple-zeta basis: split



 SPLIT: Orbitals with angular momentum L= 0



 SPLIT: Basis orbitals for state 5s



 SPLIT: PAO cut-off radius determined from an

 SPLIT: energy shift=  0.02 Ry

 p



izeta = 1

  lambda =1.00

  rc =7.295971

  energy =   -0.258275

 kinetic =0.254463

 potential(screened) =   -0.512738

potential(ionic) =   -3.626001

 WARNING: Minimum split_norm parameter:  0.15392. Will not be able to
 generate orbital with split_norm =  0.15000

 See manual for new split options

 ERROR STOP from Node:0




 =

 =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

 =   EXIT CODE: 256

 =   CLEANING UP REMAINING PROCESSES

 =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

Re: [SIESTA-L] MD.VariableCell and routine constr issue

[Mostafa Shabani]

Hi
use GeometryConstraints
fore example

%block GeometryConstraints
cellside c
cellangle alpha beta gam
position from -1 to -10
rigid 1 2
center 1 2 0.0 0.0 1.0
stress 4 5 6
routine constr
%endblock GeometryConstraints


On Sun, Jun 15, 2014 at 1:04 AM, xu yuehua xu11249...@gmail.com wrote:


 Hi,all:

 i want to relax the geometry of the cell, but i only need relax the c
 cellside, and fix the a, b side.

 according to the manual;

 i rewrite the cinstr.f the code is

 *! and J.M.Soler, 1996-2006.*
 *! *
 *! Use of this software constitutes agreement with the full conditions*
 *! given in the SIESTA license, as signed by all legitimate users.*
 *!*
 *c $Id: constr.f,v 1.6 2003/06/23 09:46:16 ordejon Exp $*

 *  subroutine constr( cell, na, isa, amass, xa, stress, fa, ntcon )*
 *c **
 *c User-written routine to implement specific geometric constraints,*
 *c by orthogonalizing the forces and stress to undesired changes.*
 *c Arguments:*
 *c real*8  cell(3,3): input lattice vectors (Bohr)*
 *c integer na   : input number of atoms*
 *c integer isa(na)  : input species indexes*
 *c real*8  amass(na): input atomic masses*
 *c real*8  xa(3,na) : input atomic cartesian coordinates (Bohr)*
 *c real*8  stress( 3,3) : input/output stress tensor (Ry/Bohr**3)*
 *c real*8  fa(3,na) : input/output atomic forces (Ry/Bohr)*
 *c integer ntcon: total number of positions constr. imposed*
 *c **
 *  implicit none*
 *  integer  na, isa(na), ntcon*
 *  double precision amass(na), cell(3,3), fa(3,na),*
 * . stress(3,3), xa(3,na)*

 *c Write here your problem-specific code.*
 *  stress(1,2) = 0.0d0*
 *  stress(1,3) = 0.0d0*
 *  stress(1,1) = 0.0d0*

 *  stress(2,1) = 0.0d0*
 *  stress(2,2) = 0.0d0*
 *  stress(2,3) = 0.0d0*

 *  stress(3,1) = 0.0d0*
 *  stress(3,2) = 0.0d0*
 *c  stress(3,3) = 0.0d0*
 *  return*

 *  end*

 am i right?

 my question is in the fdf input file, Should i set the MD.VariableCell =T

 and also Set
 %block GeometryConstraints
 routine constr
 %endblock GeometryConstraints


 or set the latter only, let the  MD.VariableCell =F

 i need your help

 thanks very much!
 --
 unl chemistry department

[SIESTA-L] TB-trance proplem

[Mostafa Shabani]

Hi dear transiesta users:
I am transiesta user.I don't know why? when i calculate current in Spin
Polarized mode for pure non magnetic structure the down current is doubled
rather than up current .I think it is not true.T(E) (transmission function)
respect to E for both up and down current is exactly same, but current are
different, How knows about the problem to help me with this.
thanks in advance
best regards
Mostafa
Sincerely Yours

Re: [SIESTA-L] spin polarization only with semicore states

[Mostafa Shabani]

Hi dear Camps
if you want to have Ti (4+) why you consider 3d2 in your psf and basis ?
i thing you have to consider just 3s2 and 3p6 orbitals.
if you want to have non ionic Ti (pure Ti) why you don't consider 4s2
orbital?


On Mon, Apr 7, 2014 at 6:47 PM, I. Camps ica...@gmail.com wrote:

 Hello SIESTers,

 I am working with TiO2.

 I build the pseudopotential file for Ti considering an atom with charge 4+
 and with semicore states.

 My procedure was (all files attached):
 - Create the INP considering the semicore states 3s2 and 3p6 (full
 occupied) and the valence states 3d2 and 4s2 (empty).
 - Generate the pseudos using ATOM
 - Generate the Ti basis using the gen-basis program from the utilities
 folder (SIESTA/Util).
 - Run the calculation.

 From the log file I got a total spin polarization (Qup-Qdown) equal to
 7.998213.

 I used two type of exchange-correlation functionals (PBE and van der
 Waals) with the same results.

 If I remove the semicore states, I got zero spin polarization.

 Is it ok? How can I explain this results?

 Best regards,

 Camps

Re: [SIESTA-L] Questions about geometry optimization

[Mostafa Shabani]

first of all you relaxed your whole structure by siesta not transiesta
.after relaxation you choose first z component of your structure positrons
 as a left electrode in electrode fdf file and do electrode calculation by
transiesta to generated electrode name.TSHS file.if both left and right
electrode is the same one calculation in enough but if both of them are
different you have do another transiesta calculation for right lead or
electrode to generate another electrode name.TSHS file for right one. The
electrode must be oriented along the z-axis and the unit cell along the
z-direction must be large enough so that orbitals within the unit cell only
interact with a single nearest neighbor cell (the size of the unit cell can
thus be derived from the range of support for the orbital basis
functions).after electrode calculation you put electrode name.TSHS file to
SR directory and define all position in fdf file for SR region and do
another transiesta run to generate scattering region.TSHS file.after that
you put both of TSHS file (generated by electrode and scattering region
calculation ) in TBtrance directory and do final calculation by tbtrans not
transiesta to earn current.


On Tue, Apr 8, 2014 at 5:54 PM, Chengbo Zhu cz...@uowmail.edu.au wrote:


 Dear SIESTA users,

 I am a little confused using TranSIESTA.

 It is advised that the geometry of scattering region(SR) should be
 optimised in SIESTA before calculating its transmission in TranSIESTA.

 My questions are:

 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in
 TranSIESTA when calculating the transmission. (I ran several testing model,
 the SR is optimized again in TranSIESTA)

 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to
 a non-zero number in Transiesta)

 3. what is the difference between 1 and 2. In a TranSIESTA run, the
 Hamiltonian matrix of SR (and atomic force) is calculated first using
 SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the
 point to run optimization of SR in SIESTA separately from TranSIESTA.

 Any thoughts would be appreciated.
 Thank you in advanced.

 Regards,
 Chengbo

Re: [SIESTA-L] Band Structure

[Mostafa Shabani]

WriteBands  T



On Thu, Feb 20, 2014 at 8:18 PM, Suman Chowdhury sumanchowdhur...@gmail.com
 wrote:

 Dear all,
 To plot the band structure which is to be set true, WriteBands or
 WriteKBands or both.

 --



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

Re: [SIESTA-L] Convergence

[Mostafa Shabani]

On 12/19/13, Suman Chowdhury sumanchowdhur...@gmail.com wrote:
 Dear all siesta user,
 How do I know if my molecular dynamics simulation is converging or not?

Hi dear Suman
when you face with   outcoor:  Relaxedatomic coordinates
(Ang).in your output file.

Re: [SIESTA-L] Maximum dynamic memory allocated problem

[Mostafa Shabani]

Hi dear Gregorio
can you tell me how to run one program in tow or more different machines.
On 12/19/13, Gregorio García Moreno gjgar...@ujaen.es wrote:
 Hi all
 I'm running one jobs in two different machines.
 In the first one, such job works without problems.
 however the second one i obtaine the next:
 New_DM. Step: 1
 Initializing Density Matrix...

 InitMesh: MESH =   270 x   200 x   162 = 8748000
 InitMesh: Mesh cutoff (required, used) =   200.000   201.285 Ry

 * Maximum dynamic memory allocated =36 MB

 And the jobs stops.

 I think the problem in the second machines is realted with the memory
 capacity. However, it machine have arond  6TB of available memory.
 Besides the machine tecnhician told me that it is not a memory related
 problem.
 Then, where is the problem in the second machine???

 Thanks in advance
 Gregorio

 --
 Gregorio García Moreno, PhD
 e-mail: gjgar...@ubu.es
 Department of Chemistry
 University of Burgos
 Plaza Misael Bañuelos s/n
 09001 Burgos - Spain

Re: [SIESTA-L] BUG report, tbtrans in development version (TBTrans_rep)

[Mostafa Shabani]

Hi Dear Andersen:
For TBT trance computation we need  electrode.TSHS, scatter.TSHS
and scatter.TSDE, is it right? For electrode.TSHS we introduce
TS.HSFileLeft./electrode.TSHS  and   TS.HSFileRight
  ./electrode.TSHS  in input file of TBTtrance but my question is how the
code understand about   scatter.TSHS and   scatter.TSDE? Is needed to
introduce them in input file? If yes please tell me how?

Excuse me another question that i have is for each  TS.Voltage i have to
repeat my calculation for scatter for getting  scatter.TSHS
and scatter.TSDE in that specific voltage for using them in TBTtrance part?

when I use transiesta to calculation a scatter region (SR) after the
electrode calculation,I have to set the TS.Voltage in the SR
inputfile! After the SR calcultion, I use the tool TBTtrans to
calculate the current and transmission, again in the inputfile I will
set TS.Voltage .MY question is :I get one current point for one
TS.Voltage set, if I want to calculate 10 points at 10 bias point,I
have to run 10 transiesta tasks for the 10 bias respectively and for
each bias I run TBTtrans to get
 10 current points? For one current point,TS.Voltage in the inputfile
for tansiesta run must be the same as the TS.Voltage in the input for
the later TBTtrans

calculation ? In the manual ,it says use the same inputfile for a
transiesta run and  TBTtrans run !



Thanks a lot



On Fri, Nov 15, 2013 at 11:19 PM, Nick Papior Andersen nickpap...@gmail.com
 wrote:

 Dear all, a colleague of mine has brought me to the attention of this bug.

 Bug occurs when:
 1) You perform a transiesta calculation with k-points.
 2) You perform a tbtrans calculation ONLY at the gamma point.

 The Hamiltonian for the device region will in the above case be wrong,
 hence the transmission and DOS will be wrong.
 I am very sorry for this.

 To be explicit:
 1) Calculate transiesta with:
 %block kgrid_monkhorst_pack
 2 0 0
 0 2 0
 0 0 2
 %endblock kgrid_monkhorst_pack

 2) Calculate tbtrans with
 %block kgrid_monkhorst_pack
 1 0 0
 0 1 0
 0 0 1
 %endblock kgrid_monkhorst_pack

 Please find a corrected source on the website (it is updated today the 15
 of November).

 Please check your calculations if the above applies to your system and
 report back if any problems occur.

 Kind regards Nick

Re: [SIESTA-L] optical mesh

[Mostafa Shabani]

Dear somayeh.
I think Armchair Graphen Nano Ribone has 2D structure .you have to pay
attention for griding (kgrid_Monkhorst)
your griding is for 1   0   00.5   1D  structure along Z Direction . Be
sure your structure is 1D or 2 D structure .And
 0   1   00.5
 0   0  32   0.5
xc.functional GGA ,   xc.authors PBE   Is better and exact approximation i
think.


On Sun, Jul 28, 2013 at 5:47 PM, somayeh rudi sapphire_b...@yahoo.comwrote:

 Dear siesta users
 I m trying to calculate the optical properties of an armchair GNR.
 can any one check my .fdf file and tell me if i defined my parameters
 correctly.specially my optical mesh.

 I  really appreciate any help.
 Best regards
 Somayeh Rudi

 here is my .fdf file:
 # AGNR N_a = 5
 #

 SystemLabel  AGNR
 NumberOfSpecies  2
 NumberOfAtoms14

 %block ChemicalSpeciesLabel
 16  C
 21  H
 %endblock ChemicalSpeciesLabel

 %PAO.Basis basis.fdf
 %PAO.BasisSize  SZ
 %block PAO.BasisSizes
 C  DZP
 H  DZP
 %endblock PAO.BasisSizes


 %AtomicCoordinatesFormat ScaledCartesian # Format for coordinates
 %AtomicCoorFormatOut Ang

 %block kgrid_Monkhorst_Pack
   1   0   00.5
   0   1   00.5
   0   0  32   0.5
 %endblock kgrid_Monkhorst_Pack

 MeshCutoff   210. Ry

 SolutionMethoddiagon

 MaxSCFIterations  200
 DM.MixingWeight   0.20
 DM.Tolerance  1.d-5
 DM.NumberPulay 4
 ElectronicTemperature  300 K

 DM.UseSaveDM true
 UseSaveData  true

 SpinPolarized false
 xc.functional LDA
 xc.authorsCA

 WriteMullikenPop   1
 SaveDeltaRho  .true.
 SaveRho   .true.
 SaveElectrostaticPotential.true.
 SaveTotalPotential.true.
 %block LocalDensityOfStates
-3.0520 -2.8520 eV
 %endblock LocalDensityOfStates

 %block BandLines
   1   0.00   0.00  0.   \Gamma
  200  0.00   0.00  1.   X
 %endblock BandLines

 LatticeConstant 4.26258 Ang
 %block LatticeVectors
22.82899136   0.000   0.000
0.000 16.00   0.000
0.000 0.000   1.000
 %endblock LatticeVectors

 AtomicCoordinatesFormat NotScaledCartesianAng
 %block AtomicCoordinatesAndAtomicSpecies
   8.95349397   8.   1.42086  1
   8.95349397   8.   2.84172  1
  10.18399482   8.   3.55215  1
  10.18399482   8.   0.71043  1
  11.41449568   8.   1.42086  1
  11.41449568   8.   2.84172  1
  12.64499654   8.   3.55215  1
  12.64499654   8.   0.71043  1
  13.87549739   8.   1.42086  1
  13.87549739   8.   2.84172  1
   8.   8.   0.87036  2
   8.   8.   3.39222  2
  14.82899136   8.   0.87036  2
  14.82899136   8.   3.39222  2
 %endblock AtomicCoordinatesAndAtomicSpecies

 # Calculation of dielectric function
 OpticalCalculation .true.
 Optical.Broaden  0.1 eV
 %block Optical.Mesh
   1 1 64
 %endblock Optical.Mesh
 #Optical.OffsetMesh .true.
 Optical.PolarizationType polarized
 %block Optical.Vector
 0.000 0.000 1.000
 %endblock Optical.Vector

Re: [SIESTA-L] unit cell-nanotube

[Mostafa Shabani]

you can use quantumwise trial version.
http://www.quantumwise.com/


On Mon, Jun 17, 2013 at 1:57 PM, Herbert Fruchtl 
herbert.fruc...@st-andrews.ac.uk wrote:

 Try TubeGen 
 (http://turin.nss.udel.edu/**research/tubegenonline.htmlhttp://turin.nss.udel.edu/research/tubegenonline.html
 ).

 A good starting point for CNTs in general is http://nanotube.msu.edu/.

   Herbert


 On 17/06/13 08:28, Drogar wrote:


 Dear siesta user

 Is there any Code to give us coordinate atomic of a arbitrary (n,m)
 nanotube?(Or
 any program)

 particularity in a flexible way, so that we can define it (in case of
 Graphyne-nanotubes)

 --
 BEST
 Drogar
 Fr.W Uni


 --
 Herbert Fruchtl
 Senior Scientific Computing Officer
 School of Chemistry, School of Mathematics and Statistics
 University of St Andrews
 --
 The University of St Andrews is a charity registered in Scotland:
 No SC013532

Re: [SIESTA-L] band lines

[Mostafa Shabani]

i think no .the symetry line in 1D like nanotube is gama to X or Z .
gamma, M, K, gamma is symetry lines for 2D graphene.there is no line
in this directions as i know and test it.

On 4/22/13, suf...@nmsu.edu suf...@nmsu.edu wrote:
 Dear Siesta Users,

 I have a basic question concerning band lines of carbon Nanotubes, it is
 correct to use the graphene band lines gamma, M, K, gamma in the case of
  chiral nanotubes (9,2), or BZ folding (2D to 1D) has to be considered by
 rolling graphene into Nanotubes? any suggestions will be appreciated,
 thanks

 regards,
 sufian alnemrat

Re: [SIESTA-L] Request about a semi-core pseudopotential of gallium

[Mostafa Shabani]

http://icmab.cat/leem/siesta/Databases/Pseudopotentials/Pseudos_GGA_Abinit/Ga-3d_html/Ga-3d.html



On Tue, Mar 5, 2013 at 11:40 AM, 隆小江 longxiaojiang@163.com wrote:

 dear siesta users,
 I'm calculating structures of some gallium based clusters with siesta
 code, but I don't have the semi-core pseudopotential of gallium, and it's
 hard for me to make and test the semi-core pseudopotential.
 Could you send me your semi-core pseudopotential of gallium (with
 electrons of  3d orbital include).
 I would appreciate it very much!

Re: Re : [SIESTA-L]

[Mostafa Shabani]

thanks .i 'll try it


On Thu, Jan 31, 2013 at 9:23 PM, karim rezouali rezoual...@yahoo.fr wrote:

 Dear Mostafa,

 Try like this


 for (9,0) GaNNT
 %block LatticeVectors
19.6758   0.  0.
0.0   19.6758000  0.
0.0   0.  1.
 %endblock LatticeVectors

 Latticeconstant 5.8500 Ang

 and

 %block LatticeVectors
30.4832   0.  0.
0.0   30.4832000  0.
0.0   0.  1.000
 %endblock LatticeVectors

 Latticeconstant 3.3775 Ang

 Good luck!!

 Karim



 Dear siesta users,


 I simulated pure GaN nanotube unit cell at 300 K by GGA approx. But I
 think the band gap and band structure that I plot is not rational.
 I'll send you my fdf and band structure pictures of my files. please
 help me what is the problem of my fdf files.


 thanks in advance,

 M. Sha'bani,

Re: Fw: [SIESTA-L] why my running did stop.

[Mostafa Shabani]

hi miss talebi.
 how can i ask my question like you from siesta mailing list
i have problem with my fdf file.i register to mailing list but i can not
see my questions and answer to them
please help mr thanks.


On Tue, Jan 15, 2013 at 7:55 PM, Abraham Hmiel abehm...@gmail.com wrote:

 I found the line,

 # MD.NumCGsteps  550  # Number of CG steps for

 which is out-commented. (550 steps is very large, by the way! Try 20 or 30
 at a time)

 Remove the '#' to perform a geometry relaxation. If you don't specify the
 number of steps, the computer will just assume I am going to do a
 single-point energy calculation. Also, because you are simulating a
 molecule (a graphene flake passivated by H, it seems), you do not need
 nearly as many k-points as you are using and the band lines you are using
 don't really make any sense because of the 0D symmetry.

 Also, you might want to upgrade to the latest version of SIESTA. Go to the
 home page for the newest release. http://icmab.cat/leem/siesta/

 Best,

 On Tue, Jan 15, 2013 at 9:47 AM, Zahra Talebi talebi_z2...@yahoo.comwrote:



  hi every body,
 I attached my out file after running a siesta, can any body explain for
 me that why the running stoped.
 best regurds




 --
 *Abraham Hmiel*
 Katherine Belz Groves Fellow in Nanoscience
 Xue Group, College of Nanoscale Science and Engineering at SUNY Albany
 http://abehmiel.net/about