[SIESTA-L] Lowdin charges

Hi all, Is there any post-processing utility to extract Lowdin charges for Siesta that anyone knows of? Best, Marcos

[SIESTA-L] Translation of PSML to psf format?

Hi all, I'd like to use the full relativistic pseudos of Pseudo Dojo in my calculations, but I'd also like to avoid having to compile the latest trunk version in the cluster I'm using right now. Is there any tool to convert the PSML pseudos from Pseudo Dojo to the old psf format? Best regards, M

[SIESTA-L] Warning in Siesta 4.1-b3 ("connected supercells may have changed")

Hi all, I am running a geometry relaxation of a Cu2N@Cu(100) slab with a Fe atom on top, comprising 235 atoms - fixed cell, not variable cell. All went well until at one point during the CG optimization, I got the following warning: WARNING: Connected supercells may have changed: [in]/[out] 215

Re: [SIESTA-L] Question about output of total spin in spin-orbit calculation

Dear Prof. Auluck, This is not the case. I am referring to the total spin magnetization of all atoms in the cell so it cannot be the case. Moreover, I have only one Fe atom in the cell, which is responsible for almost all of the spin magnetization. Best, Marcos On Fri, May 25, 2018 at 5:08 AM,

[SIESTA-L] Question about output of total spin in spin-orbit calculation

Dear all, I am performing my first spin-orbit calculations for a Fe atom over a Cu2N/Cu(100) slab. By the end of the calculation, Siesta prints a table with sqrt^2 for each of the atom in the supercell, the sum of all sqrt^2, and at the end of the calculation, the total spin. What I get is, for t

[SIESTA-L] OMM.LongOutput bug?

Hi all, I am trying out OMM released in the 4.0 beta version, and it is really amazing how faster it is with respect to diagonalization. However, I see two possible issues there. (I am testing it on a phonon calculation). 1) There seems to be a small bug in one of the variables, namely OMM.LongO

Re: [SIESTA-L] Question about fatbands

Silly, silly me! Now it works perfectly. Thanks, Nick. Marcos On Tue, Dec 1, 2015 at 9:14 PM, Nick Papior wrote: > Try use the bands.WFSX file instead. > > 2015-12-02 0:06 GMT+01:00 Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.com>: > >> Hi Nick, >&g

[SIESTA-L] Question about fatbands

Hi all, I am a bit confused about the output of a fat bands calculation. I have calculated the band structure for my system, with the options for generating the necessary output for "fat". Problem is, after using eigfat2plot, the x-axis scale is completely different from that of the band structur

[SIESTA-L] Doubt in COOP calculation

Hi all, I have a doubt in a COOP calculation. I have performed a calculation for an ethene molecule (C2H4), and the EIG file indicates that the Fermi level is -4.9449 eV. According to this Fermi level, the HOMO would be at -6.41786 eV. Therefore, if I integrate the DOS up to -6.41786 eV, I should

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

ri, Sep 25, 2015 at 11:15 AM, Nick Papior wrote: > I think so, I have not tested. > > I think none of the codes in the last couple of releases have any changes > in the affected files. > > 2015-09-25 16:08 GMT+02:00 Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.c

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

. >> Any way it seems weird that it "suddenly" triggers as all memory have >> been allocated. >> >> Could you also attach the fdf files? >> -- >> >> Kind regards Nick Papior >> On 25 Sep 2015 02:34, "Marcos Veríssimo Alves" < >&g

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

smoothly till the 19954 suggests something not directly > related to the code? Do you have disk space? > > PS. Which options did you recompile with? > > 2015-09-24 17:20 GMT+00:00 Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.com>: > >> Hi all, >> >>

[SIESTA-L] SIGSEGV fault while writing COOP data

Hi all, I am trying to write data for a COOP analysis. I have to go to a very high number of k-points, otherwise the curves (PDOS, for example) are rather "noisy", with pretty wild wigglings. The problem is, for some reason, it seems that wwave does not handle the number of k-points I'd like to h

Re: [SIESTA-L] Ignoring ghost states with vdW functionals?

ble to pass the ghost state detection. I will start the process for the LMKLL functional now, but I suspect the same will happen. Could there be a bug in the XC library, or somewhere else? Best regards, Marcos On Wed, Sep 2, 2015 at 5:05 PM, Marcos Veríssimo Alves < marcos.verissimo.al..

Re: [SIESTA-L] Ignoring ghost states with vdW functionals?

On Sep 2, 2015, at 1:17 PM, I. Camps wrote: > > Hello, > > I generated the vdW pseudos with trunk-458 with the DRSLL and LMKLL > functionals without the ghost problem for H, C, O and N. I used the INP > files from SIESTA pseudopotentials webpage. > > > []'s, > > @

Re: [SIESTA-L] Ignoring ghost states with vdW functionals?

functionals without the ghost problem for H, C, O and N. I used the INP > files from SIESTA pseudopotentials webpage. > > > []'s, > > @mps > > On Wed, Sep 2, 2015 at 4:06 PM, Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.com> wrote: > >> H

[SIESTA-L] Ignoring ghost states with vdW functionals?

Hi all, I am trying to generate pseudos for H with the vdW functionals and use them in vdW calculations using trunk-462 for the H2 molecule. However, I am running into ghost states when I try running the calculation for the H2 molecule with the DRSLL, LMKLL, C09 and BH functionals. I tried using

Re: [SIESTA-L] Bug with monoclinic cells?

27;m messing up with something here inadvertently. Cheers, Marcos On Fri, Aug 21, 2015 at 5:29 AM, Emilio Artacho wrote: > Hi Marcos > > The k-point sampling would in general be different. Are > both calculations well converged in k points? > > Emilio > > On Aug 21, 2

[SIESTA-L] Bug with monoclinic cells?

Hi all, I am running some calculations for a 3D structure made of carbon, using Siesta 3.2-pl-5. The executable was compiled with gfortran using mpif90 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic however, I am running th

Re: [SIESTA-L] DM, Qtot, Tr[D*S]

ld not be an > issue. > > > > 2015-04-16 17:46 GMT+02:00 Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.com>: > >> Hi all, >> >> I have been performing some calculations for graphene-like materials >> using the trunk-462 version, and I have

[SIESTA-L] DM, Qtot, Tr[D*S]

Hi all, I have been performing some calculations for graphene-like materials using the trunk-462 version, and I have been obtaining some warnings at the beginning of some SCF cycles: Note: For starting DM, Qtot, Tr[D*S] = 10. 10.09624902 These warnings disappear as the structure

Re: [SIESTA-L] Occupation of electronic states

Ciao Feffe, Siesta can print Mulliken charges - I guess it's the closest to what you need. Just add *WriteMullikenPop 1* to your input, and it will print the Mulliken charges at the end of every CG step. Cheers, Marcos On Wed, Mar 28, 2012 at 1:54 PM, Federico Iori wrote: > Hi all. > > Maybe

Re: [SIESTA-L] compile siesta 1.3f

pack.f >> @echo "==> Compiling dc_lapack.a in Libs..." >> @(cd Libs ; $(MAKE) dc_lapack.a) >> *#* >> version: >> @echo >> @echo "==> Incorporating information about present compilation >> >> then i error was the same >> >>

Re: [SIESTA-L] compile siesta 1.3f

Mohammad, I also have the same setting as you, and didn't have any problems compiling 1.3f1, at least not in this part. I remember, though, that I also had this problem when I first tried to compile it. It's likely that you could have your problem solved by replacing the entries in lines 153 and 1

Re: [SIESTA-L] SimulateDoping option

Natalia, You are correct in saying that all codes do add a compensating background to charged systems. However, without the SimulateDoping option, the background added is homogeneous, while with the abovementioned option, "This background charge is constant at points of the mesh near the atoms, a

Re: [SIESTA-L] Platina is non-magnetic or what it the ATM_POP?

Hi Andrei, Just one comment. If I'm not mistaken, the default spin polarization for Siesta, when you don't specify anything, is that one atom is initialized with spin up and the other down, in this case - an antiferro configuration. The final spin of the system could be non zero in this case, I su

[SIESTA-L] Palladium with van der Waals functional

Hi all, I am trying to do calculations for bulk (fcc) Pd using the van der Waals functional parametrized by Klimes et al (vk in atom, KBM in siesta, as in JPCM 22, 022201 - 2009). I have generated my own pseudo and I just can't obtain the results for the lattice constant described in PRB 83, 19513

Re: [SIESTA-L] pt.psf error

Guys, If this pseudo has been used before, it most likely doesn't present ghost states. If it did, Siesta would have stopped. So one possibility for these ghost states is that the compiler options are such that wrong results are being output. This is especially strong in ifort. If it is ifort, I r

Re: [SIESTA-L] pt.psf

Heiko, One comment on pseudopotentials. Usually pseudopotentials are not optimized for a particular problem. They are created to be good for any kind of problem. This is done by setting cutoff radii which yield the softest possible potential with good agreement of the pseudo-eigenenergies and loga

Re: [SIESTA-L] problem in reading .MD file

It should be readable by a suitable Fortran code, even if it is stored unformatted. Check the manual for the WriteMDHistory flag: http://www.icmab.es/siesta/manuales/manual-3.0-b/node83.html#3035 and also the Util folder for possible utilities to read and convert the MD files to other formats, as w

Re: [SIESTA-L] to read the value of position and velocity in in .MD file

If you don't tell us what the problem is in some detail, no one will ever be able to help you. Please state the problem in a more detailed way. Marcos On Mon, Oct 24, 2011 at 6:01 AM, Surjeet Chandel wrote: > dear siesta users > There is a problem in reading the position and velocity in .MD file

Re: Re[4]: [SIESTA-L] restart with increased kpoint set

+ p*V (eV/cell) -5787.5740 > Target enthalpy (eV/cell) -5814.1462 > > ------ > > 22 октября 2011, 17:52 от Henrik Löfås : > > Dear Maxim, > > Another point, you set > MaxSCFIterations 0 > I am not sure but I think this means that you just get you

Re: Re[2]: [SIESTA-L] restart with increased kpoint set

Maxim, I believe Chun has a point here, and I beg to differ from what you say. For some materials, it is important to include special k-points, so as to get a correct band structure and (eventually) forces - the most "famous" case would perhaps be graphene, with its K point. Even if your material

Re: [SIESTA-L] The relation between the m(=-2,-1,0,1,2) and the d orbitals ( dxy,dyz,dxz,dz2 and dx2-y2)

Check the list archives... This has come up a few months ago. Look for an answer by José Soler, more specifically. Marcos On Fri, Oct 14, 2011 at 10:20 AM, Yusia Rosee wrote: > Dear All, > > I am quite confused about the relation about the quanbum numbers > m(=-2,-1,0,1,2) and the d orbitals (

Re: Re: [SIESTA-L] Negative value in phonon spectrum

Hi all, My three cents on the subject. Graphene needs a very dense in-plane sampling for a correct description of its physical properties. It is likely that bilayer graphene does need a high sampling as well. Since it's an isolated bilayer, it would be fine to use just 1 MP division in the direct

Re: [SIESTA-L] Force units

Hector, looks like you have missed this post: http://www.mail-archive.com/siesta-l@uam.es/msg00735.html > On Thu, 18 Mar 2010 09:58:15 -0500, Backlund, Daniel wrote > > The forces are in eV/Ang (per iofa.f) > > > > Daniel J. Backlund > > Texas Tech University - Physics > > daniel.backl...@ttu.ed

Re: [SIESTA-L] Slab convergence problems

In addition to Andrei's and Slimane's suggestions, I'd increase the mesh cutoff. You have too few atoms to justify such a low cutoff, and a finer mesh could help in the convergence. Keep the electronic temperature high from the beginning, increasing it if necessary until you reach convergence in th

Re: [SIESTA-L] Graphene with stress-tensor-Voigt elements less than 0.01 kBar

Piotr, One possible reason is that your convergence parameters are not sufficiently strict. DM convergences of 10^-3 will give you very poor results. Ideally, the DM convergence should be as strict as possible, and you can easily get down to 10^-5 or even 10^-6 with systems as easy to handle as gr

Re: [SIESTA-L] graphene

Zahra, Again Andrei's remark applies: what exactly do you understand by "wrong"? Marcos On Fri, Sep 2, 2011 at 8:26 AM, Zahra Talebi wrote: > hi, > Thanks for your answer, > I have a question, > YOu know puting the kgrid cutoff just affect my DOS and make its result > wrong. but I have the cor

Re: [SIESTA-L] About LDA+U

Ye-Fei, Indeed there are people who say that adding U to O 2p orbitals is meaningless. However, I remember there is a paper on the subject by Anisimov himself (and co-authors), in http://arxiv.org/abs/cond-mat/0009107 . In this paper, they justify the application of U to O 2p states by stating (if

Re: [SIESTA-L] got a question about meshcutoff vs.convergence

Coming back to Lily's first question, it seems that a space between the word total and the = sign was forgotten: "Total =" instead of "Total=". Marcos On Thu, Aug 4, 2011 at 12:26 PM, Hongyi Zhao wrote: > On 08/04/2011 05:50 AM, apost...@uni-osnabrueck.de wrote: > >> This is not in the flags; t

Re: [SIESTA-L] CG optimizing problem. geometries in .STRUCT_NEXT_ITER file

Krishna, Do you have the same problem for smaller systems? Most probably fdf files are useless in this case, since it is a compiler problem. My wild guess: check if you are using optimization O3. If you are, then lower it to O2. Marcos On Thu, Jul 28, 2011 at 4:45 AM, krishna Mohan Grangadhran P

Re: [SIESTA-L] orderN problem

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 On Thu,

Re: [SIESTA-L] DM.AllowExtrapolation for VariableCell Structural relaxation optimization.

This variable sets an extrapolation of the density matrix to the new set of coordinates in a relaxation process, after an SCF cycle ends. It is hopefully a better starting, than just using the DM from the previous step at the end of the SCF cycle. It is independent of variable cell or relaxation me

Re: [SIESTA-L] Can siesta do the Superconductivity study?

Check work by Xavier Blase. It hasn't been necessarily done with Siesta, but if I remember well, he calculates the electron-phonon coupling strength for some superconductivity formula. From his paper, you will know what you need, and it will be easier for people to figure out if what you need can b

Re: [SIESTA-L] the homogeneous neutralizing background

The paper I've suggested before deals exactly with this question. > > Cheers > > NH > > > 2011/7/18 Marcos Veríssimo Alves > >> As far as I remember, the first approach is used in siesta (adding a >> neutral background). However, this only works well, in pr

Re: [SIESTA-L] the homogeneous neutralizing background

As far as I remember, the first approach is used in siesta (adding a neutral background). However, this only works well, in principle, for cubic (simple, bc and fc), for which Madelung corrections are properly implemented. To check this properly, run a test calculation with a net charge, just so yo

Re: [SIESTA-L] question about post-process output file .PDOS

pdosxml. On Fri, Jul 15, 2011 at 11:27 PM, lily zheng wrote: > Thanks, It seems there is no ready-made one like eig2dosto > handle.PDOs? > > Lily > > > On Fri, Jul 15, 2011 at 4:11 PM, wrote: > >> > Dear all, >> > >> > How to give those parameters which show up as the head of .PDOS file?

Re: [SIESTA-L] anything wrong with this input file?

Perhaps %block AtomicCoordinatesAndAtomicSpecies52006 <<=== ? Marcos On Thu, Jul 14, 2011 at 11:01 PM, lily zheng wrote: > Dear all, > > I got so confused about this run. Usually if everything is okay, the last > line is "end of run, time" . > > But this one is without "end of run

Re: [SIESTA-L] The meaning of 2Pdxz, 2Pdxy, 2Pdx2-y2, and so on.

Should stand for Polarization. Notice it has higher angular momentum (l=3). Marcos On Thu, Jul 14, 2011 at 2:04 PM, Hongyi Zhao wrote: > Hi all, > > I let siesta write out the wavefunction for graphene and then I use the > readwfx utility to extract the information from graphene.WFSX. > > Then

Re: [SIESTA-L] Br Pseudopotential

You must add the 3d electrons explicitly to your basis set in the block PAO.Basis. Check the manual and the list archives - a few years ago I have written a rather extended email explaining these things. Cheers, Marcos 2011/6/27 Gregorio García Moreno > ** > Sorry, but I have obtained the same

Labels and magnetic quantum numbers (was Re: [SIESTA-L] The PDOS analysis)

Hi Gao, It is not very trivial to deduce this, and I have struggled with it a bit. But the correspondence between orbital quantum numbers and labels is: p: m=-1 -> x m=0 -> z m=1 -> y d: m=-2 -> x^2-y^2 m=-1 -> yz m=0 -> z^2 m=1 -> xz m=2 -> xy It's even good to have thi

Re: [SIESTA-L] How to interprete x-axis in bands-file?

As far as I remember, the way siesta does the division of the x-axis from one point to the other is to calculate the length of the vector joining the initial and final points in k-space, then divide this length by the number of points along the direction, defining a delta_l for the direction consid

Re: [SIESTA-L] graphene band structure

Sorry, I made a mistake here. It should be K=(0.5, -0.5, 0) instead. Marcos 2011/6/14 Marcos Veríssimo Alves > It has nothing to do with Hydrogens in the system. As a matter of fact, > hydrogens would open the gap - it would be graphane, not graphene. The input > seems fine to me,

Re: [SIESTA-L] graphene band structure

It has nothing to do with Hydrogens in the system. As a matter of fact, hydrogens would open the gap - it would be graphane, not graphene. The input seems fine to me, and it it most likely because your specification of band lines is incorrect. If you choose BandLinesScale ReciprocalLatticeVector

Re: [SIESTA-L] Are these test failures significant?

with the code... > Any idea of the performance hit taken by not using atlas? > > Thanks! > Carlos > > 2011/6/10 Marcos Veríssimo Alves : > > When it comes to energies, it seems that some of them are too different. > Try > > compiling without atlas (that is, no libra

Re: [SIESTA-L] Are these test failures significant?

When it comes to energies, it seems that some of them are too different. Try compiling without atlas (that is, no libraries, just the siesta libs) and if that doesn't work, try lowering the optimization level. Also, compile siesta with the flag -DGRID_DP - that could make some difference. Best reg

Re: [SIESTA-L] siesta + Ifort 12?

Thanks for the info, Jesús. There's no need to make any benchmark, I just wanted to know if it was worth trying to install ifort 12 at all :) Marcos 2011/6/9 Jesús Carrete Montaña > On 09/06/11 16:23, Marcos Veríssimo Alves wrote: > > Jesús, > > > > Thanks fo

Re: [SIESTA-L] siesta + Ifort 12?

Jesús, Thanks for sharing. A few questions: 1) What mpi are you using? How is it compiled? 2) Do you have benchmarks to compare with previous versions of ifort (10.x, 11.x) and perhaps other compilers in the same processors? Best regards, Marcos 2011/6/9 Jesús Carrete Montaña > On 09/06/11 1

Re: [SIESTA-L] LDAU problem

d Mn basis set from the siesta website. Best of luck, Marcos On Mon, Jun 6, 2011 at 4:49 PM, silvia wrote: > Sorry, > > this is the correct fdf file > > > > El 06/06/2011, a las 16:17, Marcos Veríssimo Alves escribió: > > Silvia, > > There is too little information o

Re: [SIESTA-L] LDAU problem

Silvia, There is too little information on your problem for anyone to say anything meaningful. But, no, in principle there are no such problems - I am doing calculations using Siesta LDAU using semicore states and U and I get no such error. Marcos On Mon, Jun 6, 2011 at 4:08 PM, silvia wrote:

Re: [SIESTA-L] Obtain the atomic orbital contribution to HOMO at special k point.

Perhaps in your case the best thing to do is a COOP analysis. It could in principle show you which states are more bonding and which are not: check http://www.cohp.de (and the bibliography therein, of course) for more details. Hope this helps, Marcos On Mon, May 30, 2011 at 9:43 PM, Hongyi Zhao

Re: [SIESTA-L] variable cell

Not necessarily. Set MD.TargetPressure to the desired value (0.01 GPa, f.e.). Marcos On Thu, May 19, 2011 at 2:52 PM, akshu hans wrote: > Dear users > when i try to relax the technetium unit cell using MD.VariableCell T, the > forces on atoms relax to less the 0.04ev and stress tensor is close

Re: [SIESTA-L] About the specifications for fdf file.

Indeed, these lines (the ones with ==) shouldn't be there. Or, at least, they should have a hash (#) in the beginning, in which case Siesta would interpret them as a comment and it would have no effect. Marcos On Thu, May 19, 2011 at 1:29 PM, Hongyi Zhao wrote: > 2011/5/19 Valentin V. Karas

Re: [SIESTA-L] A Fundamental Doubt

Make an xsf file including the translation vectors (check the XCrysDen documentation on the website for how to do it, or use Andrei Postnikov's tool). Then, in XCrysDen, increase the number of repetitions in the direction you want. If yout structure appears continuous, then it is correct (in princi

Re: [SIESTA-L] Visualization of crystal structure

xcrysden is great. Check the xcrysden documentaiton (howto) in the xcrysden website to see how to make a xsf file. You can use an xyz and struct_out files to create a xsf file without much effort. You can even use xcrysden files in Vesta fot visualization. Marcos On Thu, Apr 28, 2011 at 10:25 PM,

Re: [SIESTA-L] What is meant by .pseudos pls?

Ghous, Forget about the .pseudos file, it just means something in the context of running the tests in an automated way. The procedure for running siesta is in pages 9 and 10 of the manual, and in the tutorials available on the web. In a very simplified manner, suppose you want to run a compiled ve

Re: [SIESTA-L] issue with installing siesta 1.3p

Ram, 1) Discover what $MKL_ROOT is. If you're using a standard intel installation and ifort 11 as your arch.make suggests, it should be something like /opt/intel/Compiler/11.1/075/mkl/lib/em64t/ (check this in your system). For the sake of example, let's suppose that this is where the mkl is insta

Re: [SIESTA-L] values in .EIG are in eV?

Yes, eV. Marcos On Tue, Apr 12, 2011 at 7:01 PM, Szakacs, Csaba wrote: > Question: > > are the values from the .EIG file in eV ? > > Suggestion: > > somewhere it should mention the units in use. > > > Thanks, > Csaba > > > >

Re: [SIESTA-L] Off-topic: Vesta

x: + 598 2 924 1906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > --------- > > El 06/04/2011, a las 10:27, Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.com> escribió: > > > Hi all, >> >> So, great to know there a

Re: [SIESTA-L] Off-topic: Vesta

Hi all, So, great to know there are knowledgeable people on Vesta in the mailing list. My question is the following: I have a cubic structure, a perovskite. I have a [sqrt(2) x sqrt(2)] cell of this structure, with relaxed positions with rotated oxygen octahedra in the x-y plane only, out of which

[SIESTA-L] Off-topic: Vesta

Hi all, This has nothing to do with Siesta, strictly speaking, but it could be of general interest: supercell building. I see many people here use and like GDIS. I have tried to download and compile it once, but it didn't compile. With the executable version of GDIS that came with Ubuntu, I found

Re: [SIESTA-L] Why I cann't see the threads posted by me and the follows-ups of that thread?

That is a particular thing to gmail, I think. When my email was the academic one, I used to get my replies. But I do get follow-ups as threads to my posts on the list. Marcos On Fri, Mar 18, 2011 at 8:17 AM, Alexander Vozny wrote: > I can only see the threads by others, and cann't see the thre

Re: [SIESTA-L] Compile of the siesta-3.0-rc2 and its parallel capability.

This issue has been discussed a few days ago in the list (I myself answered it). Please check the list archives before posting a question: someone most likely has had the same problem you have had before. Marcos On Thu, Mar 17, 2011 at 3:47 AM, wrote: > Dear all, > > I compiled the siesta-3.0-r

Re: [SIESTA-L] A pseudopotential-based self-interaction correction (pseudo-SIC) scheme

This is a private implementation by the group of Stefano Sanvito, if I'm not mistaken. You'd have to contact him directly to see if he can release you the code, because it is not distributed in official Siesta releases. Marcos On Wed, Mar 16, 2011 at 5:23 PM, Alexander Vozny wrote: > > I rememb

Re: [SIESTA-L] Are siesta and transiesta able to study the Higgs Boson ?

My advice is that you read about pseudopotentials as they are used in DFT calculations (especially, what their use entails). The answer to your question lies there. Marcos On Mon, Mar 14, 2011 at 2:22 PM, gaohaiyuan wrote: > Dear siesta users: > > I intend to use DFT simulation to verify Higgs

Re: [SIESTA-L] monkhorst_pack for graphene

You forgot to include the mesh shfits. Your MP block should read x1 y1 z1 sh1 x2 y2 z2 sh2 x3 y3 z3 sh3 Usually the shifts are 0.0 or 0.5. Marcos On Sun, Mar 13, 2011 at 3:04 PM, sheetal sharma wrote: > hi, > I am working on graphene sheet and using the following in input file > it works

Re: [SIESTA-L] ifort+mpich2 compiling error

This has happened before to people using ifort 11. If this is the case, switch to ifort 10.1, and don't forget to recompile mpi with it. Marcos On Fri, Mar 11, 2011 at 9:06 AM, Reza Kalantari < rezakalantarinez...@gmail.com> wrote: > Dear Siesta Users > > I have used ifort and mpich2 to compile

Re: [SIESTA-L] ferromagnetic state

Juliana, I suppose the best you can do is to fix the spin of the system as a whole using the FixSpin and TotalSpin flags. However, there is no way to guarantee the final state of the system, at least within SIESTA - at least, none that I know of. Marcos On Fri, Mar 11, 2011 at 4:27 AM, Juliana M

Re: [SIESTA-L] problem with .bands file

It is trying to read more data than there actually is in the .bands file. I am not sure of what you are doing exactly, but the amount of data in the file, if you are creating it by hand (???) should be consistent with what you tell the program to read. Marcos On Wed, Mar 9, 2011 at 5:48 AM, deepa

Re: [SIESTA-L] Parallel_version

= 3 rc= 2.047986 el= 0.003178 Ekb= -1.649997 kbcos= -0.006611 > > KBgen: Total number of Kleinman-Bylander projectors: 16 > atom: > - > > atom: SANKEY-TYPE ORBITALS: > atom: Selecte

Re: [SIESTA-L] Parallel_version

Michael, I'm pretty sure this issue has already been discussed before on the list, but here goes the short version of the story. Siesta needs infiniband or myrinet (in general, a low latency internode connection) to work properly in parallel, otherwise you should try to run it in parallel only on

Re: [SIESTA-L] again for fermi level shift

Fen, If your calculation was done correctly, you must have made some convergence study for the thickness of the slab. Your slab should be thick enough so that the lattice parameter in the center of the slab, and the electronic structure of the center of the slab, are the same with respect to bulk.

Re: [SIESTA-L] again for fermi level shift

Gao, If you already have your O2 molecule in a box big enough so that it is already isolated from its periodic images (10, 12 Ang should do the job), there is no need to place the O2 molecule far from the surface, and all you need is the isolated O2 molecule calculation and the O2+surface calculat

Re: [SIESTA-L] Bandslines

Bohr / Angstrom conversion? On Thu, Feb 10, 2011 at 3:47 PM, pietro bonfa wrote: > Dear Siesta users, > > I have a problem that I wasn't able to overcome despite it has been largely > discussed in this mailing list. > The following BandLines block is from the input file that have been given > t

Re: [SIESTA-L] Polarization Functions

Hi Michael, "Channel" refers to angular momentum channel (I can't quite remember why it's called so, but you'll see it sometimes). So (n=2, l=0) is the 2s orbital or 2s "channel"; (n=2, l=1) is the 2p "channel" and so on. So actually, when you refer to basis sets, you should specify them, strictl

Re: [SIESTA-L] PBEsol XC functional

Ian, Are you using the PBSsol as your XC functional inside the fdf file? Ususlly this kind of warning is trying to tell you that your pseudo has been generated with a different XC functional than that which you are using for your DFT calculation, which can be rather messy. Marcos On Sat, Feb 5,

Re: [SIESTA-L] Why oxygen atom has 2d orbital?

On Mon, Jan 31, 2011 at 11:55 AM, Fen Hong wrote: > Dear Marcos > Thank you very much. > > what do you mean that "plot the complete PDOS and integrate it up to the > Fermi level". I think the integration is the total states up to the fermi > level not the number of electrons. > If I am not mista

Re: [SIESTA-L] Posible SPAM: UV-Vis spectroscopy

N, Just a remark: in principle, you can calculate transition dipole moments - this is exactly what the optical subroutine does. The formalism is in Harrison's books. However, for the UV-VIS spectra, not all of them will contribute, you will have to select the appropriate ones, or perhaps construct

Re: [SIESTA-L] structural relaxation

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 the

Re: [SIESTA-L] local density of states

I think for that, you'd have to determine the boundaries of each plane, calculate the whole LDOS and then set the elements of the LDOS(x,y,z) of the planes you don't want to zero, in case you want it just for visualization purposes. Marcos On Sun, Jan 30, 2011 at 3:57 PM, mashiat alaaii wrote: >

Re: [SIESTA-L] Why oxygen atom has 2d orbital?

Fen, Regarding the first question, this is basic Fortran90 programming stuff. Check any good Fortran programming tutorial for how a record is constructed. Orbid is a record which contains the relevant information about each contribution to the PDOS in the file: n, l, m, zeta, spin, atom number in

Re: [SIESTA-L] PDOS showing occupation in the "d" orbital in SiN

This has to do with how polarization orbitals are determined in Siesta. The subject has been discussed in the list before, I think, but in brief: in the manual, you can see that they are the solutions to the perturbation problem of an atom in a weak electric field. Now, if you look at this problem,

Re: [SIESTA-L] Results of noncollinear calculation--why magnetization always in z-direction??

Menghao, Whereas I am not sure what exactly is the setup for the angles theta and phi (that is, if theta is measured from the z axis or from the x-y plane), it could be that theta=90 degrees is already a possible energy minimum. In particular, if theta is measured from the x-y plane, then you have

Re: [SIESTA-L] pdosxml and spin information

wrote: > Hi, Marcos. > > If z refers to the zeta of the basis, now it makes sense because i'm using > the DZP ones. So the PDOS of one orbital, 2p for example, is the sum of the > two zeta contributions ? > > Thanks for your time. > > My bests, > > Weslley. >

Re: [SIESTA-L] pdosxml and spin information

Weslley, z here refers to the zetas of your basis function. If I am not mistaken, spin is denoted by s in the .PDOS files. Marcos On Fri, Jan 21, 2011 at 6:10 PM, Weslley Souza Patrocinio < wesl...@vonbraunlabs.com.br> wrote: > Hi, all. > > I'm using the pdosxml util for a system without spin p

Re: [SIESTA-L] Fw: mismatch in band structure of bulk tin in beta phase.

e easily. > Please check the input and suggest me what basis set and pseudo is suitable > for bulk Beta Sn (body centered tetragonal structure). > > Suman Kalyan Sahoo > > --- On *Wed, 19/1/11, Marcos Veríssimo Alves < > marcos.verissimo.al...@gmail.com>* wrote: > > >

Re: [SIESTA-L] Ti pseudo for TiO2 rutile and anatase

Giacomo, I see you are using a mesh cutoff of 100 Ry for your calculation. This could be too small by itself for O, which is a hard pseudo in comparison with other elements. I believe converged calculations for compound with O should use at least 180 Ry (an equivalent of 45 Ry in plane waves), wh

Re: [SIESTA-L] Fw: mismatch in band structure of bulk tin in beta phase.

Suman, could you give us a more precise idea of how the band structure, lattice parameters and cohesive energy compare with the data in the literature (that is, providing numbers and an illustration of the band structure)? With the very scarce information you provide I can only think of trivial mi

Re: 回复： [SIESTA-L] How to calculate vibrational frequencies ofmoleculewithSiesta program?

Sean, There are redirection signs ( < > ) missing in what you have typed. If you type /siesta/obj/siesta < /siesta/util/vibra/src/si.ifc.fdf > si.ifc.out it should work for real. Perhaps there is some font problem somewhere - either in Javier's file or your version of Powerpoint. Marcos. 2011/

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