[SIESTA-L] V-I characteristics using LDA+U in Transiesta

[Sonu Kumar]

Dear all,

Can V-I characteristic be studied using LDA/GGA+U formalism in Transiesta
and relevant utilities?

bests, sonu


* and With kind regards,*

*S Kumar |  PhD.*

Re: [SIESTA-L] OPTIMIZATION(ZnO)

[Sonu Kumar]

For generating pseudo-potentials (norm-conserving), use ATOM program
provided with SIESTA.
But, be careful before using them for production runs, rather first test
them (I advise to generate pseudopotentials only if it not available or the
available one does not serve the purpose you want to use for).

bests,
kumar


*With kind regards,*

*S Kumar |  PhD.*

Re: [SIESTA-L] Problem in installing siesta-4.0

[Sonu Kumar]

undefined reference
s
 to the routines of Lapack library are there => means you might not have
installed lapack
library or location of the libraries is not mentioned.

Add the location of this library in arch.make file. Similary other
libraries locations are to be added. Also, read about the installation
instructions in siesta manual.


*With kind regards,*

*S Kumar |  PhD.*
​

Re: [SIESTA-L] change DOS as increasing supercell size

[Sonu Kumar]

Increasing supercell size changes the concentration of defects, that is why
you see
changes in DOS.

bests,
sonu


*===*
With kind regards,
Dr. S Kumar, Post doctoral fellow
Physical Sciences and Engineering  Divison,
IBN Sina Building, KAUST,
Thuwal, KSA
*===*

On Tue, Aug 8, 2017 at 3:55 PM, MB MB  wrote:

> Dear SIESTA users,
>
> I really need your help. I am studying defects in MoS2 2D structures.
> As I increase the size of the supercell from 5*5 to 8*8, the position of
> defects states changes in DOS diagram
>
> I use DZP basis set and default values to create orbitals.
> Is there any suggestion why this happens and how to fix it?
>
> Best regards
> Mohammad Bahmani
>

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.

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

[Sonu Kumar]

​Dear manjeet,
​

For spin polarized calculations I need pseudopotential of Pt.

Pseudo potential does not contain informations about spin, and  are​

​not generated with spin.
Spin is added by using some tag in SIESTA, please see the spin DFT.

Please let me know how can i find pseudopotential of this configuration [Xe]
 4f14 5d9 6s1  for Pt?

​Why do you need f states in valence?
d states should be taken in vale​nce.

Here is Pt.inp for atom taken from :
http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/Pseudos_LDA_Abinit/Pt_html/Pt.html
-
   pg -- file generated from Pt ps file
tm2
   Pt   ca
 0.000 0.000 0.000 0.000 0.000 0.000
   124
60 1.000 0.000#6s
61 0.000 0.000#6p
52 9.000 0.000#5d
53 0.000 0.000#5f
   2.6   2.73000   2.6   2.6   0.0   0.0

#23456789012345678901234567890123456789012345678901234567890  Ruler
--
Clearly, it takes 6s and 5d states as valence states.
Try to generate pp form this file, and test it. Also, read the atom
manual.

hope it helps.

sonu



 Regards,

 manjeet

Re: [SIESTA-L] Hubbard Parameter

[Sonu Kumar]

​You have to take different values of U/J and see whic​
​
​h one of them
correctly describes physical properties, says Band gap, JT distortion etc.​


hope it helps!!​


On Thu, Jun 19, 2014 at 3:46 PM, Anita Rani ranianit...@gmail.com wrote:

 Hello to all Siesta Users.


 .
 Can anyone tell me please about Hubbard (U) Parameter. How we can
 calculate it from Siesta output files. In some papers it is mentioned
 that U = The separation of energy level
 due to coulomb interaction energy between the Majority 3d and minority 3d.
 In case of Mn it is 5U. because there are 5 valence electrons at 3d levels.

 i.e. 5U = The separation of energy level  due to coulomb interaction
 energy between the Majority 3d and minority 3d.

 How we can calculate The separation of energy level  due to coulomb
 interaction energy between the Majority 3d and minority 3d.

 Please Help me.

 Thanks






 --

// \\  Anita Sharma
   //   \\ Assistant Professor in Physics
  // ... \\Guru Nanak College for Girls
 //   \\   Sri Muktsar Sahib, (Punjab)
 (9465305760)

Re: [SIESTA-L] GGA pseudopotential of Cr ,Fe ,Mn

[Sonu Kumar]

Did you try this ?
http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-gga-abinit.html!!!

regards,
sonu



On Wed, May 28, 2014 at 9:12 AM, Swati Khatta swati.kha...@gmail.comwrote:

 Dear siesta Users,

 I am working on the magnetic properties with GGA approximation using
 siesta-3.1. But I am not getting good results of my calculations Please
 provide me the correct input file of GGA pseudopotential of  Cr, Fe ,Mn.
 I'll be thankful of your positive response .

 Regards
 swati

Re: [SIESTA-L] Magnetism from Charge Density

[Sonu Kumar]

HI,

To study magnetism, you have to do spin-polarized calculations, where
you will get spin up charge density (rho_up(r)) and spin down charge
density (rho_down(r)),
and then finally magnetization density ~ (rho_up(r)-rho_down(r)).

hope it helps !!

sonu



On Fri, Mar 28, 2014 at 1:11 AM, I. Camps ica...@gmail.com wrote:

 Hello,

 Until my knowledge, the charge density is not directly related to
 magnetism.

 Magnetism is related to spin distribution, not to charge distribution.


 []'s,

 @mps


 On Thu, Mar 27, 2014 at 1:15 PM, zehab sohbatzadeh zeh...@yahoo.comwrote:

 Hi suman
 First you should define in fdf file as attach file and see it with
 rho2xsf.there are useful information in attach presentation.

 best regards
 Zihab Sohbatzadeh,
 PhD Student,
 Dept. of Physics,
 Faculty of Science,
 Ferdowsi University of Mashhad ,
 Mashhad ,
 Iran .
 Mobile: +98 9153490795
 Phone: +98 511 8818534
 Fax : +98 511 8796416


   On Thursday, March 27, 2014 4:37 PM, Suman Chowdhury 
 sumanchowdhur...@gmail.com wrote:
  Dear all,
 How to estimate magnetism from charge density in siesta?

 --



 *Junior research fellow  Dept. of Physics, University of
 Calcutta Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*

Re: [SIESTA-L] regarding k point sampling

[Sonu Kumar]

Dear Amar,

You can check by yourself as what should be the k-mesh for sampling the
k space in your system.

For a nano-ribbon, k point grid could be AxAx1, with nano-ribbon along Z
direction.
where, A range from 2, 3, 50, 60,  and so on depending upon the
size of the system and  convergence conditions.

It would be much better, if your read relevant papers about the
nano-ribbons.
one could be http://arxiv.org/pdf/1001.4407.pdf

hope it helps.

regards,
sonu
IITD





 * *


On Fri, Sep 20, 2013 at 10:07 AM, Dr. Amar Bahadur amar.b@gmail.comwrote:


 Dear siesta users,
  Is there any helpful link that could provide
 the k-point sampling of graphene nanoribbon?
 --
 Kind Regards.

 ==
 Dr. Amar Bahadur
 (Department of Physics)
 Kamla Nehru Institute of Physical and Social Sciences,
 Sultanpur- 228 118 (U.P.) India
 Email: amar.b@gmail.com amar.b@gmail.com
 Mob.-+91-9451431428

Re: [SIESTA-L] Re : Defining lattice constant of CrC6

[Sonu Kumar]

 waring of too close atom ,,here is my fdf file plz help me out


clearly you have defined your atoms to be close to each other.

Check with the xcrysden and any other visualization software.

Further, how many formula units of CrC6 are there in your hexagonal
cell ?

Also, it's better if you paste your input file rather than attaching it.

hope it helps.

regards,
sonu
IITD

Re: [SIESTA-L] what should be meshcut off energy

[Sonu Kumar]

Hi,

I think better you  start with 70 ryd mesh cutoff, and go
for k point convergence test, and then see the convergence
of total energy or the properties you are interested in.

regards,
SKumar
IITD

On Fri, Jun 1, 2012 at 5:02 PM, Henrik Löfås henrik.lo...@fysik.uu.sewrote:

 Dear sir,

 Have you checked which mesh cutoff is actually used? Somewhere in your
 output file you will find something like

 InitMesh: Mesh cutoff (required, used) =

 Probably for the ranges where the total energy is constant the used mesh
 cutoff will have the same value? The mesh cutoff is not a
 continuous variable, so when doing the convergence test you have to check
 which mesh cutoff is actually used.

 Best regards
 Henrik


 2012/6/1 mamta chauhan mamta_phys...@yahoo.co.in

 Dear sir

 Thanks for your reply. The problem that i found in selecting mesh cut of
 is that
 the total energy is constant for cetain ranges of mesh cut energy is
 constant like in 70 Ryd to 110 Ryd it is -296.671577. Then from 120 Ryd to
 140 Ryd it is -296.683935 so on.

 Tahnks
 Mamta
 --- On *Fri, 1/6/12, arun dhiman arun242...@yahoo.com* wrote:


 From: arun dhiman arun242...@yahoo.com
 Subject: Re: [SIESTA-L] what should be meshcut off energy
 To: siesta-l@uam.es siesta-l@uam.es
 Date: Friday, 1 June, 2012, 4:15 PM


 You can take value more than 110 Ry for which energy converges

 Arun Kumar
 Research Scholar
 Deptt of Physics
 Himachal Pradesh University
 Shimla-5
 Himachal Pradesh
 India
   --
 *From:* mamta chauhan mamta_phys...@yahoo.co.in
 *To:* siesta-l@uam.es
 *Sent:* Friday, 1 June 2012, 14:58
 *Subject:* [SIESTA-L] what should be meshcut off energy

 Dear Users

 I am applying the convergence test  for NaCl crystal.For that I took mesh
 cut off energy from 30 Ryd onwards.I found that after 70 Ryd total energy
 was constant upto 110 Ryd. on increasing the mesh cut off further the total
 energy became constant. I would like to know what value of mesh cut off
 should be selected.

  Thanks
 Mamta

Re: [SIESTA-L] lattice constant optimization

[Sonu Kumar]

Dear Nibras Mossa Umran,

i do not know whether your message is in urdu or in any other language?

Please convey your message in english so that whole of the SIESTA community
can understand it.

Thank you very much !!!

regards,
SK
IITD,India





2011/12/28 nibras mossa nibrasmo...@gmail.com:
 السلام عليكم  ممكن تتحدث معي بالعربية انا اعمل على نفس الكود اشرح لي مشكلتك
 بالتفصيل وانشاء الله نستطيع الايجاد الحل لها


 On Sat, Dec 17, 2011 at 2:47 PM, majid fathiyan mfathiya...@gmail.com
 wrote:

 in the name of God
 I am sorry for not explaining about my question, it is because of my
 weakness in english,
 I am working on cu(111) slab. I have 15 layer, and I want to optimize
 my lattice constant. but I don`t know how to do it correctly.
 I tried to change my lattice constant and calculate the total energy
 and draw the diagram of lattice constant according to total energy but
 the lattice constant which have the smallest total energy is so biger
 that my experimental lattice constant.
 so if any body knows how can I optimize my lattice constant please let me
 know.
 thank you.




 --
 Nibras Mossa Umran
 PhD,Research Scholar
 Panjab University
 Chandigarh
 India.

Re: [SIESTA-L] how the solve such problem?

[Sonu Kumar]

Hi,

I would suggest to first try your own generated pseudo-potentials to
have a better control over your calculations.

ATOM code in siesta doesn't generate psedopotentials with
multiple projectors.

To add addition projector corresponding to a specific state, you
have to use KB projectors flag (if i remember correctly) in your .fdf
input file. Please see the manual.

Good Luck.

S. Kumar
IITD


On Thu, Dec 15, 2011 at 7:32 AM, aqingchen artingc...@yahoo.com.cn wrote:

Hi, everbody,
 When I use the pseudoptentials file from the (
 http://www.icmab.es/dmmis/leem/siesta/Pseudopotentials/periodictable-intro.html)
 to calculate some cases. But some errors come up as follows:

 GHOST: No ghost state for L =  3
 KBgen: WARNING: Ghost states have been detected
 KBgen: WARNING: Some parameter should be changed in the
 KBgen: WARNING: pseudopotential generation procedure.
 ERROR STOP from Node:0

 how to solve this problem? please give me some suggestions !
 Thank you !

Re: [SIESTA-L] Water vibrational frequencies

[Sonu Kumar]

Dear Prathibha Ramaprasad all siesta users,

Your Mesh cutoff is very small. Increase it.

Long ago i tried to calculated water molecule frequencies.
Here is the calculated vibrational frequencies and eigen vectors :


k= 0.000.000.00
Eigenvector  = 1
Frequency=-0.186036
Eigenmode (real part)
  0.6470E+00 -0.6857E+00  0.1405E-02
  0.1618E+00 -0.1714E+00  0.3503E-03
  0.1618E+00 -0.1714E+00  0.3519E-03
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00 -0.E+00
Eigenvector  = 2
Frequency= 0.025870
Eigenmode (real part)
  0.2328E-02  0.4128E-02  0.9428E+00
  0.5820E-03  0.1032E-02  0.2357E+00
  0.5820E-03  0.1032E-02  0.2357E+00
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00 -0.E+00
Eigenvector  = 3
Frequency= 0.240529
Eigenmode (real part)
 -0.6857E+00 -0.6470E+00  0.4526E-02
 -0.1714E+00 -0.1618E+00  0.1130E-02
 -0.1714E+00 -0.1617E+00  0.1133E-02
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00 -0.E+00
Eigenvector  = 4
Frequency=54.689888
Eigenmode (real part)
  0.1887E+00 -0.8071E-03 -0.2385E-03
 -0.3752E+00  0.5643E+00  0.1524E+00
 -0.3797E+00 -0.5611E+00 -0.1514E+00
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
Eigenvector  = 5
Frequency=80.272376
Eigenmode (real part)
  0.4023E-01 -0.9692E-04 -0.1125E-02
 -0.7505E-01  0.1259E+00 -0.6883E+00
 -0.8587E-01 -0.1255E+00  0.6928E+00
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00 -0.E+00
Eigenvector  = 6
Frequency=   331.224078
Eigenmode (real part)
 -0.1211E-02 -0.2622E-02  0.E+00
  0.2838E-02  0.8284E-02 -0.6688E+00
  0.2005E-02  0.2205E-02 -0.6644E+00
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
Eigenvector  = 7
Frequency=  1558.552499
Eigenmode (real part)
 -0.1121E-02 -0.2768E+00 -0.2081E-02
 -0.3918E+00  0.5558E+00  0.1377E-02
  0.3962E+00  0.5513E+00  0.6946E-02
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00 -0.E+00
Eigenvector  = 8
Frequency=  3718.259590
Eigenmode (real part)
 -0.1399E-02 -0.1857E+00 -0.1618E-02
  0.5899E+00  0.3690E+00  0.7151E-02
 -0.5843E+00  0.3739E+00 -0.6774E-03
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00 -0.E+00  0.E+00
Eigenvector  = 9
Frequency=  3879.361876
Eigenmode (real part)
 -0.2718E+00  0.1545E-02 -0.1800E-02
  0.5445E+00  0.4062E+00  0.6856E-02
  0.5426E+00 -0.4124E+00  0.3437E-03
Eigenmode (imaginary part)
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00  0.E+00
  0.E+00  0.E+00 -0.E+00

with regards,



On Thu, Sep 8, 2011 at 1:17 AM, Prathibha Ramaprasad prama...@asu.eduwrote:

 Hi Andrei,

 These are the frequencies I get:

 eigenvalue #   1  omega=  -445.13301743729897
   eigenvalue #   2  omega=  -110.38569520939947
   eigenvalue #   3  omega=  -46.712013030918499
   eigenvalue #   4  omega= -1.12145510233318604E-002
   eigenvalue #   5  omega=  1.10614378824742104E-002
   eigenvalue #   6  omega=  1.36483674814901548E-002
   eigenvalue #   7  omega=   67.336297669281663
   eigenvalue #   8  omega=   115.87202534402807
   eigenvalue #   9  omega=   317.70618567755037
  Zero point energy = 0.031055 eV

 Also attached here are the input files.

 Thank you for your help.

 Prat

 On Tue, Sep 6, 2011 at 11:03 PM, apost...@uni-osnabrueck.de wrote:

 Dear Prat:
 what are your (nine) frequencies, in fact?
 How close to zero are six of them?
 100 Ry cutoff a priori seems too light ...

 Best regards

 Andrei Postnikov


  Hi Siesta users,
 
  When I ran a vibra tool for water, I am getting ridiculously low values.
  From what I see in the code, it seems to be converting the frequencies
 to
  cm^-1 before it outputs to the file, but it looks more like the numbers
  are
  in THz. I am using GGA, 100Ry mesh cutoff and 1 molecule of water in a
  20X20X20 box.
 
  Has anyone here able to obtain anything close to expt values? Any
  pointers?
 
 
  Thank you,
 
  Prat
 



==
Sonu Kumar
Phd Student,Physics Department
Indian Institute of Technology ,Delhi-110016, India
https://profiles.google.com/1009ukumarweb:-http://www.iitd.ac.in/
==

Re: [SIESTA-L] unable to reduce stress tensor components below 1.0 GPa ?

[sonu kumar]

Respected Prof. Emilio Artacho,

Thank you very much for helpful suggestions.

Also, few questions :

is it good  idea to apply EQUAL confinement to all atomic orbitals
of different atoms in  a system ?  Because we are adding same
soft confinement potential to all different atomic Hamiltonians to
generate the basis functions and its like equally exciting all pseudo-
states in these pseudo-atoms.

What criteria should i use to decide the soft confinement potential
to generate numerical atomic orbitals in a multi-atom system?


To all siesta users,

   Solution: increase mesh cutoff. You can also add soft confinement to your
orbitals. And/or filter them.

 is there any option related to  filtering of atomic orbitals is siesta. I
am
using siesta-2.0.2.


With regards,

-- 
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/

[SIESTA-L] unable to reduce stress tensor components below 1.0 GPa ?

[sonu kumar]

Dear all siesta users,

i am trying to relax cell parameters in rhombohedral unit cell.

But stress tensor components are not becoming less than 1.0
GPa. However pressure is ~zero.

part of output is:-

Stress-tensor-Voigt (kbar):  -61.58   29.02   32.56
-23.03   -3.31  -13.80
siesta: Pressure (static):
siesta:   0.00120848 -0.00280164  kBar

I used these options:-

MD.MaxStressTol  1.0 GPa
MD.TargetPressure  0.0 GPa
%block MD.TargetStress
-1.0 -1.0 -1.0 0.0 0.0 0.0
%endblock MD.TargetStress

What should i do to reduce it?

Also, interesting thing is that off diagonal stress components are non-zero,
but should be zero. Is this explainable?

Thank you.

regards,
Sonu
IITD

[SIESTA-L] Very slow or no convergence of density matrix ?

[sonu kumar]

Dear all siesta users,
 after varying
DM.MixingWeight =0.1, 0.01
,0.001,
DM.NumberPulay   4, 6, 8
DM.NumberKick  0,10, 20,40
DM.KickMixingWeight  0, 0.10,
0.01

scf iterations=400
   Meshcutoff=500 Ry and MP grid
=6x6x6  is used.

  i am still not able to get the
convergence.

  Part of output file with very slow
convergence :

siesta:  284   -31598.9061   -31598.9016   -31598.9016  0.0011 -1.9863
siesta:  285   -31598.9061   -31598.9025   -31598.9025  0.0011 -1.9862
siesta:  286   -31598.9061   -31598.9027   -31598.9027  0.0011 -1.9862
siesta:  287   -31598.9061   -31598.9024   -31598.9024  0.0011 -1.9863
siesta:  288   -31598.9061   -31598.9049   -31598.9049  0.0011 -1.9870
siesta:  289   -31598.9061   -31598.9055   -31598.9055  0.0011 -1.9872
siesta:  290   -31598.9061   -31598.9079   -31598.9079  0.0011 -1.9875
siesta:  291   -31598.9061   -31598.9079   -31598.9079  0.0011 -1.9874
siesta:  292   -31598.9061   -31598.9085   -31598.9085  0.0011 -1.9871
siesta:  293   -31598.9061   -31598.9076   -31598.9076  0.0011 -1.9871
siesta:  294   -31598.9061   -31598.9078   -31598.9078  0.0011 -1.9871
siesta:  295   -31598.9061   -31598.9077   -31598.9077  0.0011 -1.9871
siesta:  296   -31598.9061   -31598.9066   -31598.9066  0.0011 -1.9871
siesta:  297   -31598.9061   -31598.9059   -31598.9059  0.0011 -1.9870
siesta:  298   -31598.9061   -31598.9075   -31598.9075  0.0011 -1.9865
siesta:  299   -31598.9061   -31598.9073   -31598.9073  0.0011 -1.9865
siesta:  300   -31598.9061   -31598.9074   -31598.9074  0.0011 -1.9865
siesta:  301   -31598.9061   -31598.9061   -31598.9061  0.0012 -1.9897
siesta:  302   -31598.9061   -31598.9073   -31598.9073  0.0011 -1.9873
siesta:  303   -31598.9061   -31598.9072   -31598.9072  0.0011 -1.9873
siesta:  304   -31598.9061   -31598.9071   -31598.9071  0.0011 -1.9871
siesta:  305   -31598.9061   -31598.9079   -31598.9079  0.0011 -1.9870
siesta:  306   -31598.9061   -31598.9072   -31598.9072  0.0011 -1.9871
siesta:  307   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9870
siesta:  308   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9872
siesta:  309   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9871
siesta:  310   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9871
siesta:  311   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta:  312   -31598.9061   -31598.9071   -31598.9071  0.0011 -1.9870
siesta:  313   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9871
siesta:  314   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  315   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta:  316   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta:  317   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta:  318   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  319   -31598.9061   -31598.9065   -31598.9065  0.0011 -1.9870
siesta:  320   -31598.9061   -31598.9067   -31598.9067  0.0011 -1.9871
siesta:  321   -31598.9061   -31598.9061   -31598.9061  0.0012 -1.9873
siesta:  322   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9870
siesta:  323   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9870
siesta:  324   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta:  325   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  326   -31598.9061   -31598.9067   -31598.9067  0.0011 -1.9870
siesta:  327   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9870
siesta:  328   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9871
siesta:  329   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  330   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  331   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9870
siesta:  332   -31598.9061   -31598.9076   -31598.9076  0.0011 -1.9870
siesta:  333   -31598.9061   -31598.9064   -31598.9064  0.0011 -1.9870
siesta:  334   -31598.9061   -31598.9067   -31598.9067  0.0011 -1.9871
siesta:  335   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9871
siesta:  336   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  337   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  338   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9871
siesta:  339   -31598.9061   -31598.9074   -31598.9074  0.0011 -1.9870
siesta:  340   -31598.9061   -31598.9067   -31598.9067  0.0011 -1.9870
siesta:  341   -31598.9061   -31598.9061   -31598.9061  0.0012 -1.9874
siesta:  342   -31598.9061   -31598.9068   -31598.9068  0.0011 -1.9871
siesta:  343   -31598.9061   -31598.9071   -31598.9071  0.0011 -1.9870
siesta:  344   -31598.9061   -31598.9072 

Re: [SIESTA-L] Very slow or no convergence of density matrix ?

[sonu kumar]

Dear Marcos, Pablo and Jw ,

i had used the DM obtained from 1000K and used that with 0K, but i got the
error in
dimension of maxnd as:

iodm: Reading Density Matrix from files
chkdim: ERROR: In iodm, dimension maxnd =   94363. It must be at least
109536
Stopping Program from Node:0
chkdim: ERROR: In iodm, dimension maxnd =   82707. It must be at least
95742
chkdim: ERROR: In iodm, dimension maxnd =   78200. It must be at least
90692
chkdim: ERROR: In iodm, dimension maxnd =   55290. It must be at least
66436
chkdim: ERROR: In iodm, dimension maxnd =   58695. It must be at least
64950
Stopping Program from Node:4
chkdim: ERROR: In iodm, dimension maxnd =   62895. It must be at least
71914
Stopping Program from Node:5
Stopping Program from Node:3
Stopping Program from Node:1
Stopping Program from Node:2

with regards,
Sonu

2010/6/9 Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com

 This could be due to degeneracies in your system. The system could be
 jumping from two different electronic configurations with the same energy
 and it cannot decide in which one to stay. Follow Pablo's suggestion, raise
 the electronic temperature - not excessively, especially if you are dealing
 with spin polarization. Once converged, slowly lower the electronic
 temperature until you get to the low value you aim for.

 Marcos


 On Wed, Jun 9, 2010 at 4:47 PM, jw wei redsky...@gmail.com wrote:

 The problem have puzzled me for a long times.

 2010/6/9, Pablo A. Denis pab...@fq.edu.uy:
  perhaps increasing the electronic temperature can help.
 
  best regards,
 
  pablo
- Original Message -
From: sonu kumar
To: siesta-l@uam.es
Sent: Wednesday, June 09, 2010 10:37 AM
Subject: [SIESTA-L] Very slow or no convergence of density matrix ?
 
 
Dear all siesta users,
 after varying
DM.MixingWeight =0.1,
  0.01,0.001,
DM.NumberPulay   4, 6, 8
DM.NumberKick  0,10, 20,40
DM.KickMixingWeight  0,
 0.10,
  0.01
 
scf iterations=400
   Meshcutoff=500 Ry and MP
 grid
  =6x6x6  is used.
 
  i am still not able to get the
  convergence.
 
  Part of output file with very
 slow
  convergence :
 
siesta:  284   -31598.9061   -31598.9016   -31598.9016  0.0011 -1.9863
siesta:  285   -31598.9061   -31598.9025   -31598.9025  0.0011 -1.9862
siesta:  286   -31598.9061   -31598.9027   -31598.9027  0.0011 -1.9862
siesta:  287   -31598.9061   -31598.9024   -31598.9024  0.0011 -1.9863
siesta:  288   -31598.9061   -31598.9049   -31598.9049  0.0011 -1.9870
siesta:  289   -31598.9061   -31598.9055   -31598.9055  0.0011 -1.9872
siesta:  290   -31598.9061   -31598.9079   -31598.9079  0.0011 -1.9875
siesta:  291   -31598.9061   -31598.9079   -31598.9079  0.0011 -1.9874
siesta:  292   -31598.9061   -31598.9085   -31598.9085  0.0011 -1.9871
siesta:  293   -31598.9061   -31598.9076   -31598.9076  0.0011 -1.9871
siesta:  294   -31598.9061   -31598.9078   -31598.9078  0.0011 -1.9871
siesta:  295   -31598.9061   -31598.9077   -31598.9077  0.0011 -1.9871
siesta:  296   -31598.9061   -31598.9066   -31598.9066  0.0011 -1.9871
siesta:  297   -31598.9061   -31598.9059   -31598.9059  0.0011 -1.9870
siesta:  298   -31598.9061   -31598.9075   -31598.9075  0.0011 -1.9865
siesta:  299   -31598.9061   -31598.9073   -31598.9073  0.0011 -1.9865
siesta:  300   -31598.9061   -31598.9074   -31598.9074  0.0011 -1.9865
siesta:  301   -31598.9061   -31598.9061   -31598.9061  0.0012 -1.9897
siesta:  302   -31598.9061   -31598.9073   -31598.9073  0.0011 -1.9873
siesta:  303   -31598.9061   -31598.9072   -31598.9072  0.0011 -1.9873
siesta:  304   -31598.9061   -31598.9071   -31598.9071  0.0011 -1.9871
siesta:  305   -31598.9061   -31598.9079   -31598.9079  0.0011 -1.9870
siesta:  306   -31598.9061   -31598.9072   -31598.9072  0.0011 -1.9871
siesta:  307   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9870
siesta:  308   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9872
siesta:  309   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9871
siesta:  310   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9871
siesta:  311   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta:  312   -31598.9061   -31598.9071   -31598.9071  0.0011 -1.9870
siesta:  313   -31598.9061   -31598.9070   -31598.9070  0.0011 -1.9871
siesta:  314   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9870
siesta:  315   -31598.9061   -31598.9069   -31598.9069  0.0011 -1.9871
siesta

[SIESTA-L] Trivial problem with conversion from fractional to Bohr coordinates?

[sonu kumar]

Dear all siesta Users,

sorry fof trivial question...

i want to convert  fractional coordinates  to Bohr coordinates in fcc
primitive unit cell.

Lattice constant (conventional cell) =10.104 ang.

Siesta does following conversion ...

siesta: Atomic coordinates (Bohr) and species
siesta:  0.0   0.0   0.0
siesta:  7.16018  11.93363   9.54690
siesta: 11.93363   9.54690   7.16018
siesta:  9.54690   7.16018  11.93363

outcoor: Atomic coordinates (fractional):
0.0.0.
0.50000.75000.2500
0.75000.25000.5000
0.25000.50000.7500

But  i got ..
0.0   0.0   0.0
6.752  10.1285  3.3762
so on...

why this differencecan anyone assist me?

with regards,
Sonu

[SIESTA-L] not able to download pseudo-potentials from user contributed data base?

[sonu kumar]

hi dear all siesta users,

I am not able to download the Psedo-potentials(PPs) from the user
contributed database.

how can i download them ?

With Regards,
Sonu Kumar

Re: [SIESTA-L] underestimated zone center frequencies in MgO ?

[sonu kumar]

Dear Sir,

*your structure is not exactly cubic* (look at your atoms position).
 I wonder why you use atomic coordinate which looks like
 the result of relaxation along with lattice parameters
 which look like given by hand. Relax either both, or none.


1) i relaxed both atomic coordinates and lattice parameters using variable
cell option and got

outcoor: Relaxed atomic coordinates (scaled):
0.59930.61100.5744   1  Mg 1
0.485531110.485535230.48553182   2  O  2

outcell: Unit cell vectors (Ang):
   -0.222.0448032.044814
2.044808   -0.262.044818
2.0448032.044802   -0.21
so i used lattice constant=4.089606~4.09 Ang.

2) when i did study of energy v/s volume, i got minima at 4.10 Ang, with out
above relaxation.
should i proceed this way, keeping care of symmetry or should i see the
final results(freqs) to decide, which one to use (relaxation or no
relaxation)?

3) can we use macroscopic polarisation analysis for small band gap
 materials? sorry, if my question is stupid.

With Due Regards,

Sonu Kumar

Phd Student
Indian Institute of Technology Delhi
Delhi-110016
web:-http://www.iitd.ac.in/

[SIESTA-L] underestimated zone center frequencies in MgO ?

[sonu kumar]

Hi dear all Siesta Users,
 i tried to reproduce the zone center frequencies in MgO.
But they are not same as  shown in JOURNAL OF APPLIED PHYSICS 100,
023533,2006. In this paper, doubly degenerate freq is ~400 cm-1 and other is
~700cm-1 apart from acoustical freqs.

But Siesta calculates following freqs :

  eigenvalue #   1  omega= -5.342383622781044E-002
  eigenvalue #   2  omega=  9.129011837545617E-003
  eigenvalue #   3  omega=  4.213637115974628E-002
  eigenvalue #   4  omega=   397.442968241599
  eigenvalue #   5  omega=   413.630587428353
  eigenvalue #   6  omega=   413.916231936010

I used the basis and pp for  MgO as used by J. Junquera et al., Phys. Rev.
B, 64, 235111 (2001), available on siesta site.

I am wondering, How can i reproduce them? i am attaching the input file.

I need your help to reproduce the correct frequencies.

With due Regards,

Sonu Kumar

Phd Student
Indian Institute of Technology Delhi
Delhi-110016
web:-http://www.iitd.ac.in/


mgo.fdf
Description: application/vnd.fdf

[SIESTA-L] simplex method

[sonu kumar]

hi dear all,

Can anybody provide me some  study material or any kind of help  related to
basis optimisation by simplex method?
I have problem in understanding the variational parameters ?

With Regards,
1009u

Re: [SIESTA-L] how do you change the atomiccoordinatesformat from ang to scaledcartesian? by hand?

[sonu kumar]

Hi Fen Hong,

 use-- AtomCoorFormatOut  ScaledCartesian  with type of run=cg and cg
steps=0

regards,
1009u




On Thu, Jan 28, 2010 at 12:08 PM, Fen Hong gm030...@gmail.com wrote:

 Hi, everyone
 I am trying to change the atomiccoordinateformat from ang to
 scalecartesian.
 I calculated it by hand. But it seems impossible if the system is too
 large.
 How do you change it.Is there some simple way to do it?

 Example:
 LatticeConstant8.6514 Ang
 %block LatticeVectors
  1. 0. 0.
  -0.5 0.8660254 0.
  0. 0. 2.00
 %endblock LatticeVectors

 AtomicCoordinatesFormat Ang

 %block AtomicCoordinatesAndAtomicSpecies
 0.0.2.35460760   1   1  Au
 1.467001120.84919753   -0.23066334   1   2  Au
 2.89953753   -0.029254282.65757611   1   3  Au
 4.325690380.832479500.   1   4  Au
 5.76513068   -0.002950982.68342880   1   5  Au
 7.209483960.832479500.   1   6  Au
-1.488233092.498424832.66695348   1   7  Au
 0.3.329918010.   1   8  Au
 1.346816232.527931722.29986223   1   9  Au
 2.883793593.329918010.   1  10  Au
 4.371842462.493503082.66713826   1  11  Au
 5.767587173.329918010.   1  12  Au
-2.884964964.996297582.68129387   1  13  Au
-1.441896795.827356510.   1  14  Au
-0.016174385.035688592.66152987   1  15  Au
 1.441896795.827356510.   1  16  Au
 2.899764735.038174712.66126078   1  17  Au
 4.325690385.827356510.   1  18  Au

Re: [SIESTA-L] Re:why the forces, energy different in siesta-2.0.2 and beta version?

[sonu kumar]

hi 张广平,

I have little knowelge of mpi libraries. May be other experienced SIESTA
users help you sort out the problem. Are you sure that PGI works fine?

Perhaps code may be changed a little bit like you said, as i have compiled
both versions on same computer under same OS.

Hopefully some one on the list may help.

With Regards,

1009u


2010/1/25 张广平 zgp...@126.com

 Hi,sonu kumar
I compiled the siesta with mpich-1.2.7 copmiled using PGI.
 But for math LIB,I use mkl,I put the arch.make in the attachment.
 I guess the difference for mine is caused by the mpich when it communicate
 data.I think it can be fix by some settings for mpich,but i dont know how to
 fix it.You use two versions ,I think it maybe the parameters in the code is
 different type(float or double precision) or they were installed on two
 different machine or under two different OS.

   Guangping Zhang


  -- Original --
  *From: * sonu kumar1009uku...@gmail.com;
 *Date: * Mon, Jan 25, 2010 02:42 AM
 *To: * siesta-lsiesta-l@uam.es;
  *Subject: * Re: [SIESTA-L] Re:why the forces, energy different in
 siesta-2.0.2 and beta version?

 hi 张广平,

   I have compiled both the versions using gnu-fortran compiler
 (gfortran). You can have a look at arch.make files of these versions for
 serial run .
   I could have checked these differences for parallel versions, also.
 but, i don't have intel fortran compiler 10.0 and mkl10.1 to compile beta
 version.

 1009u

 2010/1/24 张广平 zgp...@126.com

 Hi,sonu kumar
  I have encountered the same problem,but mine was because of serial or
 parallel mode.I compiled me siesta with mpich on the REHEL-5.4.when I run a
 task using 1 or 8 or other,the results differed from each other after 4-6
 decimal places.
Are you compiled the two version with the same parameters?

[SIESTA-L] why the forces, energy different in siesta-2.0.2 and beta version?

[sonu kumar]

hi SIESTA users,

I am getting different forces,energy ( after 4-6 decimal places) in stable
and beta version of siesta.

Both the packages are compiled with gfortran compiler in serial mode and,
then, tested for  fe.fdf  file in tests/fe.

Parts of both outputs are as follows:
for stable version:

siesta: E_KS(eV) = -782.2432
siesta: Atomic forces (eV/Ang):

   Tot   -0.21   -0.01   -0.00

   Max0.21
   Res0.12sqrt( Sum f_i^2 / 3N )

   Max0.21constrained

Target enthalpy (eV/cell) -782.2458
siesta: Eharris =  -782.242590
siesta: Etot=  -782.243177
siesta: FreeEng =  -782.245753
xxx--

beta version

siesta: E_KS(eV) = -782.2434
siesta: Atomic forces (eV/Ang):

   Tot   -0.260.170.12

   Max0.26
   Res0.19sqrt( Sum f_i^2 / 3N )

   Max0.26constrained


Target enthalpy (eV/cell) -782.2460

siesta: Eharris =  -782.242770
siesta: Etot=  -782.243427
siesta: FreeEng =  -782.246003
-

Are these differences reasonable enough to affect the calculations ?

Can anybody tell me ?

With regards,

1009u

Re: [SIESTA-L] Re:why the forces, energy different in siesta-2.0.2 and beta version?

[sonu kumar]

hi 张广平,

  I have compiled both the versions using gnu-fortran compiler
(gfortran). You can have a look at arch.make files of these versions for
serial run .
  I could have checked these differences for parallel versions, also.
but, i don't have intel fortran compiler 10.0 and mkl10.1 to compile beta
version.

1009u

2010/1/24 张广平 zgp...@126.com

 Hi,sonu kumar
  I have encountered the same problem,but mine was because of serial or
 parallel mode.I compiled me siesta with mpich on the REHEL-5.4.when I run a
 task using 1 or 8 or other,the results differed from each other after 4-6
 decimal places.
Are you compiled the two version with the same parameters?





arch.make
Description: Binary data


arch.make
Description: Binary data

[SIESTA-L] Zone center phonons with unit cell or Supercell ?

[sonu kumar]

hi dear all

I want to calculate the phonons at gamma point of the BZ.

1) Do i need to make the supercell to find the phonons ? is a  unit cell is
sufficient for it?

2) which unit cell i mean whether primitive or conventional unit should i
use?



with regards,

1009U

[SIESTA-L] Stress components during atomic relaxation and Auxiliary supercell ?

[sonu kumar]

Hi dear all

I am doing *atomic relaxation* of a system containing 7 atoms in the
primitive unit cell (conventional unit cell contains 21 atoms)

1)  i got  the max. force tolerance  0.0002 eV/Ang, but stress components
seems to be large as follows:

 Stress-tensor-Voigt (kbar):   -5.09   16.77   19.82
-12.79   -3.98   -8.53

  Here i set variable cell  option  false .

  What should be the max tolerance of the stress components?


2)  if i take supecell =unit cell, even then SIESTA takes an internal
auxiliary supercell, here 6x6x5=180 atoms with non zero kgrid cutoff.
Although with zero value of kgrid

 cutoff, it doesn't take  internal auxiliary supercell. how does it
happen? Is it because of periodic boundary   condition? but boundary
condtion in SIESTA is not mentioned

 in the manual.


 can anybody help me?


With Kind Regards,


1009U

[SIESTA-L] can not do OrderN with K-points

[sonu kumar]

hi dear all,


i am doing a FC run over a system with 189 atoms in the unit cell (formed by
making use of Supercell).

but i got the error.probably bcoz of memory?

can anybody help me.?

last part of my output file is:

siesta: ==
Begin FC step =  0
Undisplaced coordinates
==

superc: Internal auxiliary supercell: 2 x 2 x 2  =   8
superc: Number of atoms, orbitals, and projectors:   1512 17928 22680

outcell: Unit cell vectors (Ang):
   15.510.000.00
   10.062640   11.8026450.00
   10.0626404.643694   10.850486

outcell: Cell vector modules (Ang)   :   15.51   15.509969   15.509792
outcell: Cell angles (23,13,12) (deg): 49.5514 49.5494 49.5499
outcell: Cell volume (Ang**3):   1986.2793

InitMesh: MESH =   192 x   192 x   192 = 7077888
InitMesh: Mesh cutoff (required, used) =   500.000   553.018 Ry

* Maximum dynamic memory allocated =   880 MB
*Cannot do O(N) with k-points.*
Stopping Program from Node:0
forrtl: severe (174): SIGSEGV,* segmentation fault occurred*
Image  PCRoutineLineSource
*libc.so.6*  7FDBED094A04  Unknown   Unknown
Unknown
siesta 006E37B3  UnknownUnknown
Unknown
siesta 00629ACF  Unknown   Unknown
Unknown
siesta 0056DC54  Unknown   Unknown
Unknown
siesta 0052930E  UnknownUnknown
Unknown
siesta 00403B7C  Unknown   Unknown
Unknown
libc.so.6  7FDBED036586  UnknownUnknown  Unknown
*
*siesta 00403A79  Unknown   Unknown
Unknown




1009u