Re: [SIESTA-L] Xcrysden
Dear Suman, Please take a look to the following link: http://conquer-ur-computer.blogspot.com/2010/12/how-to-install-xcrysden-in-ubuntu-linux.html - Mail original - De: Suman Chowdhury sumanchowdhur...@gmail.com À: siesta-l@uam.es Envoyé: Jeudi 27 Mars 2014 17:33:04 Objet: [SIESTA-L] Xcrysden Dear All, I have tried thousand times to install Xcrysden in my machine, but I failed.Can anyone tell me how to do it step by step? -- Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India. Ph no-+91-9830512232
Re : [SIESTA-L] formation energy
Dear Somayeh, Try like this: Efo = Edg − Epg − 2µI where, µI: is the half of the calculated total energy of H2 molecule Nb: also take a look to the BSSE corrections!! Hope this helps, Karim
Re : [SIESTA-L]
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 : [SIESTA-L] a request
Dear Zara, http://icmab.cat/leem/siesta/Databases/BasisSets/La/ Yours, Karim hi every body I am trying to work on a structure which have lantanium, with sithe help of siesta code so I needed Lantanium psf file. As you know siesta site doesn`t have it, I tried to generate it but I couldn`t. if any body can generat it or have it, I would be so thanksfull to have that. thank you.
[SIESTA-L] pseudopotential_for_exotic_atoms
Dear all, Is there a way to generate pseudopotential for exotic atoms such as muonic atoms? Karim
[SIESTA-L] projected_bandstructure
Dear SIESTA users, Is there a way ( utilities) to plot the partial (projected) bandstructure? Thank U in advance, Karim
[SIESTA-L] cd.psf_and_Se.psf
Dear all, Could you share with me the GGA pseudopotential file for Cd (cadmium) and Se (selenium)?. Thanks Karim
Re : [SIESTA-L] pt.psf
Dear, Here's an input pe Platinum tm2 2.5 n=Pt c=pbr 0.0 0.0 0.0 0.0 0.0 0.0 12 4 60 1.00 0.00 61 0.00 0.00 52 9.00 0.00 53 0.00 0.00 2.45 2.45 2.45 2.45 0.000.77 Karim
RE: Re : [SIESTA-L] GaN PAO.Basis block
Dear, Let me see the output file of the test you did with the PAO base (Test.out) that I have proposed and if possible the input file of gallium pseudopotential (Ga.tm2.inp). Best regards, Karim
RE: Re : [SIESTA-L] GaN PAO.Basis block
Dear,
The message is for Hashemi. I talk about the test he (she) did with the PAO
basis that I gave him to see the type of error he (she) got.
Best regards,
Karim
Dear BoXiao,
i tested all of cases,The first case is true only:
Ga 3
n=3 2 2 p 6.500 5.100
1.000 1.000
for another cases,I got the previous error message:
initatom: Reading input for the pseudopotentials and atomic orbitals --
Species number: 1 Label: Ga Atomic number: 31
Species number: 2 Label: N Atomic number: 7
Ground state valence configuration: 4s02 4p01
Reading pseudopotential information in formatted form from Ga.psf
Semicore shell(s) with 10 electrons included in the valence for
Ga
Ground state valence configuration: 2s02 2p03
Reading pseudopotential information in formatted form from N.psf
Wrong number of rc's
Stopping Program from Node: 0
best
regards,
--- On Wed, 10/19/11, BoXiao xiaoboy...@hotmail.com wrote:
From: BoXiao xiaoboy...@hotmail.com
Subject: RE: Re : [SIESTA-L] GaN PAO.Basis block
To: siesta siesta-l@uam.es
Date: Wednesday, October 19, 2011, 11:58 PM
Dear hashemy
Thanks for your reply, take the following as an example,
Ga 3
n=3 2 2 p 6.500 5.100
1.000 1.000
or
Ga 3
n=3 2 1 6.500 5.100
1.000 1.000
or
Ga 3
n=3 2 1 p 6.500 5.100
1.000 1.000
there are three type of definations, which one is right, why?
best wishesDate: Wed, 19 Oct 2011 23:45:45 -0700
From: hashemy2...@yahoo.com
To: siesta-l@uam.es
Subject: RE: Re : [SIESTA-L] GaN PAO.Basis block
Dear,
Did you mean is:
PAO.BasisSizes DZP
%block
PAO.Basis
Ga 3
n=3 2 2 p
;
6.500 5.100
1.000 1.000
n=4 0 2 p
5.291 4.728
1.000 1.000
n=4 1 2 P 1
7.142 5.921
1.000 1.000
N 2
n=2 0 2 p
3.684 2.869
1.000 1.000
n=2 1
2 P 1
4.280 2.869
1.000 1.000
%endblock PAO.Basis
--- On Wed, 10/19/11, BoXiao xiaoboy...@hotmail.com wrote:
From: BoXiao xiaoboy...@hotmail.com
Subject: RE: Re : [SIESTA-L] GaN PAO.Basis block
To: siesta-l@uam.es
Date: Wednesday, October 19, 2011, 8:10 PM
#yiv464468837 .yiv464468837ExternalClass #yiv464468837ecxyiv1904341931
.yiv464468837ecxyiv1904341931hmmessage P
{padding:0px;}
#yiv464468837 .yiv464468837ExternalClass #yiv464468837ecxyiv1904341931
body.yiv464468837ecxyiv1904341931hmmessage
{font-size:10pt;}
Dear there,
as you mentioned, %block PAO.Basis
Ga 3
n=4 0 2
#this
is 4s orbital with 2 zeta
0.000 0.000
1.000 1.000
n=4 1 2 P 1 # this is 4p orbital with DZP
0.000 0.000
1.000 1.000
n=3 2 1 # this is 3d orbital with 1 zeta
0.000 0.000
1.000 1.000
Why can not you define the three orbital under
the same DZP?
Date: Wed, 19 Oct 2011 07:37:40
-0700
From: hashemy2...@yahoo.com
To: siesta-l@uam.es
Subject: Re: Re : [
SIESTA-L] GaN PAO.Basis block
Dear Karim,
I have just tryed it but I got the previous error message,but when i tested:
%block PAO.BasisSizes
GaSZ
N DZP
%endblock PAO.BasisSizes
things seem to gone right !!
what is your opinion?
--- On Wed, 10/19/11, karim rezouali rezoual...@yahoo.fr wrote:
From: karim rezouali rezoual...@yahoo.fr
Subject: Re: Re : [SIESTA-L] GaN PAO.Basis block
To: siesta-l@uam.es
Date: Wednesday, October 19, 2011, 6:59 AM
Reyhaneh,
Try with the following PAO basis: The values will be generated from the
appropriate default values. The radii will be obtained from PAO.EnergyShift
or from PAO.SplitNorm.
For more details, see SIESTA manual (section 6.3.3 Size of the basis set).
#
PAO.BasisSizes DZP
;
%block PAO.Basis
Ga 3
n=4 0 2
0.000 0.000
1.000 1.000
n=4 1 2 P 1
0.000 0.000
1.000 1.000
n=3
2 1
nbs
p;
0.000 0.000
1.000 1.000
N 2
n=2 0 2
0.000 0.000
1.000 1.000
n=2 1 2 P 1
0.000
0.000
1.000 1.000
%endblock PAO.Basis
Good luck,
Karim
Dear Karim,
thank you for your advice,did you mean is:
%block PAO.BasisSizes
Ga SZ
N DZP
%endblock PAO.BasisSizes
RE: Re : [SIESTA-L] GaN PAO.Basis block
Rayhaneh, I said stupid things in the last message. The mistake I made was that I took SZ for Ga3d with 2 radii. I apologize The following basis should work. %block PAO.Basis Ga 3 n=4 0 2 0.000 0.000 1.000 1.000 n=4 1 2 P 1 0.000 0.000 1.000 1.000 n=3 2 1 0.000 1.000 N 2 n=2 0 2 0.000 0.000 1.000 1.000 n=2 1 2 P 1 0.000 0.000 1.000 1.000 %endblock PAO.Basis
RE: Re : [SIESTA-L] GaN PAO.Basis block
It's Ok, Karim Dear Karim, Thank you very much,i tested it and everything is ok. I have a question about my last input(that its output was sent),is it wrong?
Re : [SIESTA-L] GaN PAO.Basis block
Dear, Just add a quite short single zeta for the core electrons (3d). Hope this helps, Karim Dear siesta users, I am trying to generate a DZP PAO basis for GaN while including semicore states: Ga(3d 4s 4p),but something is wrong.i checked mail archive but can not find a good solution. The error is:
Re: Re : [SIESTA-L] GaN PAO.Basis block
Reyhaneh, Try with the following PAO basis: The values will be generated from the appropriate default values. The radii will be obtained from PAO.EnergyShift or from PAO.SplitNorm. For more details, see SIESTA manual (section 6.3.3 Size of the basis set). # PAO.BasisSizes DZP %block PAO.Basis Ga 3 n=4 0 2 0.000 0.000 1.000 1.000 n=4 1 2 P 1 0.000 0.000 1.000 1.000 n=3 2 1 0.000 0.000 1.000 1.000 N 2 n=2 0 2 0.000 0.000 1.000 1.000 n=2 1 2 P 1 0.000 0.000 1.000 1.000 %endblock PAO.Basis Good luck, Karim Dear Karim, thank you for your advice,did you mean is: %block PAO.BasisSizes Ga SZ N DZP %endblock PAO.BasisSizes Best regards, Reyhaneh
[SIESTA-L] question_about_the_macroscopic_polarization
Dear SIESTA Users, As it is well known, the macroscopic polarization has an ionic and an electronic component. The electronic contribution to the macroscopic polarization is calculated using the geometric Berry phase approach. The ionic contribution, is defined as the sum of the atomic positions within the unit cell multiply by the ionic charges. Is there a way to get the the contribution of each term to the macroscopic polarization in the output file of SIESTA software?. Thanks a lot before, Karim
Re: [SIESTA-L] orderN problem
Marcos, Thank you very much for the reply: My system is a passivated (H) Si clathrate nanowire and i do not know if has a gap or not (maybe a small gap). All i kown is that the bare si46 nanowire does not have one. How to choose the following parameters for a given system: ON.ChemicalPotentialRc ON.RcLWF Karim Karim, I think OrderN works as long as your system has a gap. If your nanowire doesn't have one, you'll be in trouble there. If the first system is an isolated molecule, then it makes sense that OrderN works. If your nanowire is known to have a gap, then OrderN should work as well. Marcos
Re: Re : [SIESTA-L] vibrator calculation problem, pls help me!
Hi Yuting, For Γ-point phonons, the supercell can be just the unit cell. To my knowlege, graphen unit cell contains only 2 carbon atoms !!. (800 ) Add the lines along which band energies are calculated (usually along high-symmetry directions) For gamma phonons BandLinesScale ReciprocalLatticeVectors %block BandLines 1 0.0 0.0 0.0 \Gamma %endblock BandLines Enjoy the results, Good luck, Karim
Re : [SIESTA-L] vibrator calculation problem, pls help me!
Dear Yuting, If i am not wrong you only want to calculate the phonon gamma. SuperCell_1 0 SuperCell_2 0 SuperCell_3 0 let me see the input file of vibrator. Karim Hi, I am trying to use vibrator to calculate the phonon dispersion of an 800-atom graphene system. Now I am trying to use the .FC file I got and the .fdf file to calculate phonon dispersion by VIBRATOR, my fdf file is listed below SystemName 800a_phonon SystemLabel 800a_phonon NumberOfAtoms 800 NumberOfSpecies 1 AtomicDispl 0.04 Bohr LatticeConstant 1.0 Ang %block LatticeVectors 44.456 -1.126 0. -1.1347 51.6733 0. 0.0 0.0 13.0 %endblock LatticeVectors AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies -1.842398 35.99136 0.000E+00 1 12.011 0.5414967 3.3957496E-002 0.000E+00 1 12.011 43.55410 33.70913 0.000E+00 1 12.011 %endblock AtomicCoordinatesAndAtomicSpecies SuperCell_1 0 SuperCell_2 0 SuperCell_3 0 Eigenvectors T after the vibrator ran, the out put file is like this: redata: System Name = 800a_phonon redata: System Label = 800a_phonon Number of Atoms = 800 Lattice Constant = 1.88973 Bohr Lattice vectors (in units of Lattice Constant) = 44.45600 -1.12600 0.0 -1.13470 51.67330 0.0 0.0 0.0 13.0 Lattice vectors (in Bohr) = 84.00970 -2.12783 0.0 -2.14427 97.64842 0.0 0.0 0.0 24.56645 recoor: Atomic-coordinates input format = Cartesian coordinates recoor: (in Angstroms) recoor: Atomic coordinates (Bohr) and species recoor: 1 -3.48163 68.01384 0.0 1 recoor: 2 1.02328 0.06417 0.0 1 . recoor: 800 82.30535 63.70105 0.0 1 lxmax = 0 lymax = 0 lzmax = 0 Number of unit cells in Supercell = 1 klines: WARNING: No k-points specified!!! Eigenvectors = True Computing Eigenvalues and Eigenvectors But there is no calculating result for Eigenvalue and Eigenvector, and no .band file at all. Is there something wrong in my fdf file? I'll really appreciate it if someone can help me out!! Thanks for your time!! Yuting
Re: [SIESTA-L] LO phonons with SIESTA
Dear SIESTA Users, I think that the inability of SIESTA to correctly describe LO phonons in polar materials such as AlN at the limit q tend to 0 is porbably due to the fact that this code uses atom-centred basis sets which fail to describe the long wavelengths near gamma well far from the the atomic centers. Karim this might be useful : http://chianti.geol.ucl.ac.uk/~dario/tutorial_phonons.tar.gz On Fri, Apr 15, 2011 at 12:48 PM, karim rezouali rezoual...@yahoo.fr wrote: Dear all, I am currently working on the phonons in the whole Brillouin -zone of bulk wurtzite AlN (VIBRA- supercell of 500 atoms) and I encounter a serious problem with LO phonons in the limit of gamma. I calculated the Born charges and the dielectric tensor (LO-TO spleeting) and the results (attached file: dipersion along gamma point- A point) do not agree with calculations reported in the litterature using other softwares (linear response method). I increased the size of the supercell (700 atoms) but no change in the shape of the LO branch was observed. Is the problem intrinsic to SIESTA because no works are available (to my knowledge) on the whole-Brillouin zone optical phonons using this code in the literature?!. Thanks in advance, Karim -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010
[SIESTA-L] LO phonons with SIESTA
Dear all, I am currently working on the phonons in the whole Brillouin -zone of bulk wurtzite AlN (VIBRA- supercell of 500 atoms) and I encounter a serious problem with LO phonons in the limit of gamma. I calculated the Born charges and the dielectric tensor (LO-TO spleeting) and the results (attached file: dipersion along gamma point- A point) do not agree with calculations reported in the litterature using other softwares (linear response method). I increased the size of the supercell (700 atoms) but no change in the shape of the LO branch was observed. Is the problem intrinsic to SIESTA because no works are available (to my knowledge) on the whole-Brillouin zone optical phonons using this code in the literature?!. Thanks in advance, Karim attachment: bulk.eps
Re: [SIESTA-L] Titanium dioxide nanotubes
Michael, It is imperative to know the general rule which states that only layered materials may have tubular forms similar to carbon nanotubes as is the case of BN, MoS2,..etc. But ZnO has no bulk layered structures and therefore tubular forms made from this materials is fundamentally different from the tube structures which can be viewed as the mapping of graphitic sheet of ZnO onto the surface of a cylinder. The appropriate model for ZnO nanotubes consists to cut hollow cylinders with a given direction out of a wurtzite (ZB) ZnO crystal. The nanobubes generated this way have atomic structures matching well the structural aspects from experiment. Karim You similar in structure with carbon or boron nitride nanotubes (honeycomb cylinders)? If so, you can just generate a cabon nanotube and manually replace the carbon atoms by the appropriate ones.
Re : [SIESTA-L] optical gap band gap ??
Dear, Is the material under study (ie, bulk amorphous silicon) has a direct electronic gap or not? Karim Hello, I calculated the band structure of bulk amorphous silicon (64 atoms tetrahedrically coordinated). I found an HOMO-LUMO band gap of about 0.7 eV. Then I performed the OpticalCalculation, but I have that the resulting imaginary dielectric function has a peak at E0.7. How is this possible? I expect that each valence-to-conduction transition must be larger than the bang-gap! Roberto
Re: [SIESTA-L] optical gap band gap ??
Roberto, The band structure appears not to be totally correct. Seeing your input file systlab.fdf, I realized that this curve is obtained under the gamma point.approximation Try to sample the Brillouin zone as follows: %block kgrid_Monkhorst_Pack 2 0 0 0.0 0 2 0 0.0 0 0 2 0.0 %endblock kgrid_Monkhorst_Pack Optical calculations: %block Optical.Mesh 2 2 2 %endblock Optical.Mesh These changes will make the calculation slightly heavier but that's the price to pay for something more accurate. I have a question regarding the choice of CG for the relaxation of your structure. In your case, it seems that the use of the molecular dynamics such as Nose, NPR,. is more appropriate. Hope this helps Karim Indirect (band structure attached) R Roberto: sorry for this question, but are you sure that this band structure corresponds to your 64-at calculation? I'd expect much more bands and much less dispersion with 64 at. supercell. (I did not count the bands per energy interval, though, so I might be wrong). Anyway: how does your total DOS look like? Best regards Andrei Postnikov In date 4/3/11 15:23:46, karim rezouali wrote: Dear, Is the material under study (ie, bulk amorphous silicon) has a direct electronic gap or not? Karim Hello, I calculated the band structure of bulk amorphous silicon (64 atoms tetrahedrically coordinated). I found an HOMO-LUMO band gap of about 0.7 eV. Then I performed the OpticalCalculation, but I have that the resulting imaginary dielectric function has a peak at E0.7. How is this possible? I expect that each valence-to-conduction transition must be larger than the bang-gap! Roberto
Re: [SIESTA-L] structural relaxation
Thanks a lot Marcos, Karim Karim, I'd say that the basis set deosn't play as much an influence on the final symmetry of the unit cell (at least in Siesta) as much as a fine real-space mesh. However, if you know which symmetrization operations on forces and stresses maintain the symmetry of a cell, then you can implement them in the file constraints.f, re-compile siesta and use %block GeometryConstraints routine constr %endblock GeometryConstraints in your fdf file.Of course, you are advised to check the manual for the exact syntax of this block, as well as the programming of the constraints in this file :) Marcos On Sun, Jan 30, 2011 at 12:03 PM, karim rezouali rezoual...@yahoo.fr wrote: Dear Users, Is there a way to relaxe both atomic positions and cell vectors ( variable cell optimization) of a given system without changing the shape of the supercell (preserving the symmetry) by a judicious choice of PAO basis sets? Karim
Re : [SIESTA-L] how to use the commandoptical.vector
Dear, when you set the electric filed direction for polarized situation, the electric field can be represented by a vector perpendicular to the direction of wave propagation. The magnetic field, too, is a vector perpendicular to the electric vector and perpendicular to the direction of propagation. If the direction of the electric field vector is constant, the polarization of the wave is called linear. There is also elliptically polarized waves ( the electric vector rotates around the axis of propagation). The elliptical polarization can be right or left in the opposite direction. If the maximum amplitude of the electric field is the same regardless of its direction, polarization is called circular (a case of elliptical polarization). Karim Dears: I am trying to use siesta's optical module to calculate graphene's optical propertities,but i am confused by the command 'optical.vector'.In the manual it says :Optical.Vector (data block): This block contains 3 numbers that specify the vector direction for either the electric field or light propagation, for a polarized or unpolarized calculation,respectively. A typical block might look like: %block Optical.Vector 1.0 0.0 0.5 %endblock Optical.Vector My question is when i set the electric filed direction for polarized situation,how can i know the propagation direction ? I'm very confused of it ,could you help me ?Thank you very much!
Re : [SIESTA-L] problems in fdf of bilayer Graphene
Dear Zahra, Try to review the coordinates of the K high symmetry point in the block BanddLine BandLinesScale pi/a # Default Value %block BandLines 1 1.1547 0. 0. \M 300 0. 0. 0. \Gamma 300 0. 1. 0. \K ** 300 1.1547 0. 0. \M %endblock BandLines BandLinesScale pi/a %block BandLines 1 1.1547005 0.000 0.000 M 35 0.000 0.000 0.000 \Gamma 35 1.1547005 0.7 0.000 K 20 1.1547005 0.000 0.000 M %endblock BandLines
Re: [SIESTA-L] How to construct Ultrasoft-pseudopotentials
Bonjour Dr. Postnikov, Je m'appelle Karim Rezouali. Je suis enseignant- chercheur à l'université de Béjaia au sein du laboratoire --- En date de : Lun 5.4.10, apost...@uni-osnabrueck.de apost...@uni-osnabrueck.de a écrit : De: apost...@uni-osnabrueck.de apost...@uni-osnabrueck.de Objet: Re: [SIESTA-L] How to construct Ultrasoft-pseudopotentials À: siesta-l@uam.es Date: Lundi 5 avril 2010, 9h15 Thank you very much. If there is no Ultrasoft pseudopotentials for siesta. Which kind of pseudopotential we usually use for the tranisition metals. Dear Fen, we use norm-conserving ones. It seems nobody use the potential on the siesta Homepage. This is a wrong impression; the database of pseudos on the Siesta site was updated exactly by people who created and used these pesudos. Moreover in publications the authors often enough exactly specify what kind of pseudopotential, radii and charge configuration they use. If you don't know better, the pseudos from the abinit database (on the Siesta site, Pseudos Bases) should be good enough. Otherwise, you generate and test you own ones, guided by the examples in the User contributed database or lectures in the Siesta tutorials. Best regards Andrei Postnikov
