[SIESTA-L] Intel MKL ERROR issue for running parallel siesta

Dear all I compiled siesta successfully. But when I run it there is following error and this error will not show when I use 2cpu. I also attached my arch.make file. does anyone know the reason? Thank you a lot Min Gao --ERROR--

Re: [SIESTA-L] How to deal with the Pseudo-potential for alkali atoms

.txt (TM pseudos form JL Martin > himself). > > On 07/05/2017 09:45 AM, Fen Hong wrote: > >> Dear Siesta-users >> >> How to deal with the Pseudo-potential for alkali atoms? >> >> As we know, there is only one electron on the valence part. >> > >

[SIESTA-L] How to deal with the Pseudo-potential for alkali atoms

Dear Siesta-users How to deal with the Pseudo-potential for alkali atoms? As we know, there is only one electron on the valence part. It seems impossible to calculate the alkali atoms ions. Also, for the heavy alkali atoms, they have a large polarizable core. Pseudo potential with just one ele

[SIESTA-L] Error of Fermid

Dear All, I am trying to calculate the cationic Lithium atoms, but got error " Fermid: Iteration has not converged. Fermid: qtot,sumq= 0.000E+000 1.037273600474796E-002 " I think that is because I am using 2s1 pseudopotential that once one electron lost, there is no electrons fo

[SIESTA-L] Error of Fermid

Dear All, I am trying to calculate the cationic Lithium atoms, but got error " Fermid: Iteration has not converged. Fermid: qtot,sumq= 0.000E+000 1.037273600474796E-002 " I think that is because I am using 2s1 pseudopotential that once one electron lost, there is no electrons fo

[SIESTA-L] SCF converge problem in Metal oxygen molecule system

Dear SIESRA USERS I am going to calculate the interaction between Pt surface and Oxygen molecule. The SCF can converge sucessfully for the Pt surface and Oxygen molecule. However, the SCF doesnot converge when put oxygen to Pt surface. Does anyone know the reason and how to solve this problem?

[SIESTA-L] build slab TiO2 (1,-1,2)

Dear all Is there anyone have the manual about how to build slab TiO2 (1,-1,2) by VESTA or AVOGADRO soft. I can build the 111 surface by Pt. http://hjklol.mit.edu/content/building-slab-geometries-catalysis-vesta Or Is there any crystal structure that I can compare ? Best wishes Min Gao Hok

[SIESTA-L] Bader Charge and Meshcutoff

Dear All, I met a problem for Bader charge calculation. The Bader charge for some atoms is highly depends on the value of mesh cutoff. There are 300 atoms in my system, what I care is charges of several atoms . However, there are 2 or 3 atoms changes oscillated with different meshcutoff, the oth

Re: [SIESTA-L] Method for fix bond length

e mass as a weight factor (similar to the > example int he manual) even though I only did an energy minimization with > CG) > > If you want a finer constraint, you'll have to add a few basic > trigonometrical calculations to limit the movement of one atom to a sphere > ar

[SIESTA-L] Method for fix bond length

Dear Siesta-users, For Cartesian coordinate, is there someway to fix bond length or angle for siesta? Best, Min

Re: [SIESTA-L] phonon calculation error

Dear Postnikov, Thank you very much. I only care about the frequency. If the electronic structure is considered, the whole system is necessary. I did some tests, it seems siesta is not so slow. So I am going to compare the whole system's frequency with part of system's. If the difference is very

[SIESTA-L] phonon calculation error

Dear Siesta developers and users, Is it possible to only calculate part of system? I am going to calculate phonon frequency of part of the molecule. There are 13 atoms in molecule. so I fix No 11 and 12 by "MD.FCfirst 11 MD.FClast 12 " When I use "Vibra" to calculate the

Re: [SIESTA-L] how does siesta define the number of wave function got by Denchar

Dear Zhao, Thank you very much. 2011/7/13 Hongyi Zhao > On 07/13/2011 11:36 AM, Fen Hong wrote: > >> Dear all, >> The output of denchar is.WF#.cube, where # is the number of the wave >> function. >> But how does siesta define this number? according to the energy

[SIESTA-L] how does siesta define the number of wave function got by Denchar

Dear all, The output of denchar is .WF#.cube, where # is the number of the wave function. But how does siesta define this number? according to the energy of each wavefunction. eg. The energy for the WF is, .WF1.cube < ,WF2.cube < .WF3.cube < .. Does anyone know that Thank you very much Gao MIn

[SIESTA-L] Wave function problem

Dear all, I tried to plot the pi orbital of O2 molecule (spin-polarized calculation). The results seems not correct. For the O2, 3σ 4σ* 5σ 1π(perpendicular) 1π( parallel )2π* for 1π(perpendicular), denchar gives the spin up and spin down wave function, but I found that the shape of spin up and spin

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

gt; 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

[SIESTA-L] The PDOS analysis

Dear all, What does the value of m stand for in pdosxml/m_orbital_chooser.f90. I am not sure how does siesta separate these orbitals. What I understand is, For example For p orbital, m=-1, 0 , 1 are px, py, pz orbital. For d orbital, m=-2, -1, 0, 1, 2 are dxy, dyz, dzx, dz2, dx2-y2 or dxy, dxz, dz2

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

And how to define this zero point energy, I donot know how to find this point for different system.

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

Dear Marcos Thanks a lot. But there is another problem that for the surface, I compared the pure surface'PDOS with surface-O2, it seems the shifting the Fermi level is not enough. Because the surface is semiconductor, siesta define the fermi level as surface's middle of HOMO and LUMO, but after ads

[SIESTA-L] again for fermi level shift

Dear all I am confused by the fermi level recently. I want to compare how the O2 2p orbital changes after it adsorbed on graphite surface. I compute the O2 and O2-surface , get fermi level separately, Ef_O2, and Ef_O2-surface. then I get O2 2p orbital by pdosxml, shift the two 2p orbital energy to

Re: [SIESTA-L] how to plot charge density by Xcrysden?

Dear Zhenyu I did not met the problem you mentioned. Did you check your coordinate? I use the same parameter for calculation and the fragment's coordinate is almost same with your whole system and use the whole.XV for your diff.RHO I hope it can help Regards, Gao Min

Re: [SIESTA-L] how to plot charge density by Xcrysden?

Dear Martin. Thank you very much for your code It works really very well and easy to understand. Thank you again Regards, Gao Min

[SIESTA-L] the problem of choosing plane by xcrysden

Dear all Can xcrysden choose the plane freely? In my case, the simulation box vector is not parallel to the molecule's plane that I am interested in, So I choose another spaning vector that parallel to the molecule's plane when I transform the *.RHO to *.XSF, after that I check the charge by Xcrysd

Re: [SIESTA-L] how to plot charge density by Xcrysden?

Dear Prof Postnikov， Martin, Herbert Thank you very much. I thought that the tools of siesta is same with gview, everything can be done directly. I think there is another way to plot charge by denchar, I am checking it, and show the result after. Thank you very much again I will be very appreciated

Re: [SIESTA-L] how to plot charge density by Xcrysden?

Dear Andrei Postnikov Thank you very much. you may wish to have a look at > http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-visual.pdf > And read Xcrysden documentation (once more): > http://www.xcrysden.org/Documentation.html > To plot a difference (of whatever), you need to provide >

[SIESTA-L] Re: how to plot charge density by Xcrysden?

I found the first problem's reason, for the 3D plot, the plane can move along the axis. The charge density we need is at the place that the density is largest. Still waiting for the second question' answer. The charge difference plotting, For example, Difference = D(MgO-surface/Au) - D (Au) - D

[SIESTA-L] how to plot charge density by Xcrysden?

Dear all 1. How to plot 3d charge density by xcrysden? I change *.RHO to .XSF file (the box is same with simulation box), and open it by xcrysden Tools> datagrid> multiply factor for spin 1 and 2 is 1.0-set isovalue (donot display isosurface)-> set palne #1 #2 and #3 after that no

Re: [SIESTA-L] Shift Fermi-level

Dear Andrei Postnikov Thank you very much again. Regards, Gao Min

Re: [SIESTA-L] Shift Fermi-level

Thank you all very much. Thank Postnikov answer my basic questions. and I am very sorry that I did not describe the problem clearly. Take another example to describe the problem, step 1, calculate DOS the free O2 molecule, step 2, put that free O2 molecule and surface together but make sure the

Re: [SIESTA-L] Shift Fermi-level

Dear Andrei Postnikov, Thank you very much. I want to know why the two figures are so different (I expected them almost be superposition) after shift the fermi level. Even 1e is added to O2 molecule, it is not reasonable that the 2p orbitals of O2, O2- is so different. How does siesta find the syst

[SIESTA-L] Shift Fermi-level

Dear all, In order to compare two different system, I tried to shift the Fermi-level to zero. For example, the 2p orbital of O2 and O2-, the fermi level is -5.9199 and 3.0895 eV separately. I shift the 2p of O2 by 5.9199 eV and O2- by -3.0895 eV. But it seems not so good because the difference is a

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

Dear all As Marcos mentioned that If an integration of the DOS up to the Fermi level in Siesta gives the total number of electrons

[SIESTA-L] The Fermi level is shifted to zero or not when mprop calculate the orbitals

Dear all, The Fermi level is shifted to zero or not when mprop calculate the orbitals ? thanks Regards Gao Min

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

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. And I have to ask another question that how to distinguish orbitals. For example, 3

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

Dear all, I have another question, how can we know the number of electrons in each orbital? Thanks

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

Dear all, I tried to generate PDOS by psodxml program. There are several points that I can not understand. First, How to find the orbital that I am interested in. In the m_orbital_chooser.f90 there are explanation, what does orbid stand for? I tried but always failed, because I donot know the orb

Re: [SIESTA-L] How to calculate vibrational frequencies of molecule with Siesta program?

Hi, I donot think siesta can give you vibrational frequencies. You can write your own program 2011/1/12 jane alam > Hello all > Let me know about How to calculate vibrational frequencies of molecule with > Siesta program? can any body send me input and output files regarding to > this problem

[SIESTA-L] the Visualization tool----gdis read the strucuture

Dear all, When I run gdis it showed " gdis.exe：5716：Gtk-warning **：The specified module couldn't be found gdis.exe：5716：Gtk-warning **：Loading TM context type 'ime' failed" and the structure showed isn't correct. For example, I calculate a molecular, while when I check it by gdis, the first step is

Re: [SIESTA-L] check *.IOCH file

Dear Alexander, Thank you very much, I tranfered the *.IOCH to *.XSF, I am trying to caclulate cbader charge density according to your blog. I have add the some charge in the core and saved the pesudo-core to the *.IOCH. while I am not so clear which part is the pesudo-core charge. Can you gvie me

[SIESTA-L] check *.IOCH file

Dear all, Is there another way to check the *.IOCH file except Plrho, because I still have problem to compile the Plrho Thank you very much Regards, Gao Min

Re: [SIESTA-L] compile the plrho

Marcos， Thank you very much. I have compiled the Pgplot by f95 since the siesta was also compiled by f95. While according to installation guide, "f95 plrho.f -lX11 -lpgplot -o plrho " and set the enviroment like this “export PGPLOT_DIR=/home/fen/pgplot export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PGPLO

[SIESTA-L] error when compile Plrho

Dear all , I compiled the siesta and pgplot by f95 I use this command “ f95 plrho.f -lX11 -lpgplot -o plrho” to compile Plrho but got error ERROR MSG In file icolor.f:179 Included at plrho.f:223 IF(J.GT.97.OR.J.LT.1)PAUSE

[SIESTA-L] compile the plrho

Dear all , I want to check the *.IOCH file while the pgplot library is nessary. The compiler should be same between the siesta and pgplot. I tried to use f95 to compile the pgplot, but failed. So I want to use g77 to compile siesta, is it possible? how to do it ? Yours, Fen

Re: [SIESTA-L] Spin Polarized calculations

yes,it depends on how many single electrons in your system. fenhong On Mon, Jul 19, 2010 at 10:01 AM, Magdalena Birowska < magda.birow...@gmail.com> wrote: > Dear Siesta users; > > I want to do Spin Polarized calculations > is it efficient to do SCF calculations for it? > I mean, do Spin

Re: [SIESTA-L] How can I use B3LYP functionality in siesta?

Hi I donot think we can use it. what we have is lyp I think On Sat, Jul 3, 2010 at 11:14 PM, Guangping Zhang wrote: > > Dear siesta users and developers: > I want to use B3LYP hybrid functionality in siesta calculation ,can anyone > tell me how can I realise it? > Thanks in advance! > 2010-07-0

[SIESTA-L] choose the core correction for pseudopotential

Dear all Does anybody know how to choose the suitable core-correction for the pseudopotential. When should we add the relativistic effect? Thank you very much. Yours, Fen

Re: [SIESTA-L] ask the unit about the MM.potential again.

Hi, Madan Thank you very much for your answer. The paper showed value with J/mol nm**6,which unit did you use for C6? It seems not the ev ang**6. And for the different atoms C6_parameter, for example, the Carbon & Hydrogen, I think we should use C6 = (C(carbon)*C(Hydrogen))**0.5 = 17.17. I donot k

[SIESTA-L] ask the unit about the MM.potential again.

Dear all, I have to ask the unit about the MM.potential again for noanswer last week. I want to know unit of C6 in MM.potental for Grimme option because the manual did not mention it. Also the meaning of the "sum of the van der Waals radii for the interacting species" is just summing up the vander

[SIESTA-L] The unit about the MM.potential

Hi all, I am trying to use the MM.potential to correct the PBE functional. There are three options for the MM.potential, C6 harm, Grimme. I tried to use the Grimme and set the parameter according to Grimme's paper like that ( J. Comput. Chem. Vol 27, 1787-1799 (2006)). In Grimme's paper, %block MM.

[SIESTA-L] 2p6 3s2 semi-core for Mg,but output showed 2p4 3s2. Why?

Dear all I tried to add the semi-core on Mg atom using GGA/PBE. There would be 8 electrons in the vanlence, while in the ouput file there is only 6electrons. I put some details about this test. I generate the PP like that: pe Mg, GGA, rcore=1.20 tm2 3.0 n=Mg c=pbr 0.0

Re: [SIESTA-L] Denchar showed wrong result., Why?

Hi,Marcos I will try to calculate it according to your suggestion. And I am also trying Alex Voznyy's code. He has modified the code which is belong to Siesta. For example, modified version of Andrei Postnikov’s XCrysDen conversion tool, rho2xsf converts to CUBE instead. And also meshsubs.F file w

Re: [SIESTA-L] Denchar showed wrong result., Why?

Marcos, I use this http://theory.cm.utexas.edu/bader/ Linux x86 (ifort) there is no need to compile it, just decompression is ok

Re: [SIESTA-L] question about Monkhorst-Pack in siesta3

Hi, Joohwi Lee The k point you use is not gamma pointI think the gamma point is 1*1*1, if you arenot sure, please use the default setting, it is also gamma point. But the main reason it runs slowly is it has too many atoms. How many cores did you use? if you make the sisesta pararel, it will he

[SIESTA-L] Denchar showed wrong result., Why?

Dear all I calculate the H2O charge density and analysize it by bader. All though the total charge is right, but the atomic charge is werid. This is the ACF.dat from bader. # X Y ZCHARGE MIN DISTATOMIC VOL ---

[SIESTA-L] error when generate the O2- Pseudopotential

Dear all I want to get the O2- Pseudopotential, valence orbital is 2s2 2p6. There still has error in the output while it worked when I tried the 2s2 2p5 3d1. Does anybody know the reason? the input is pg Oxygen tm2 2.0 n=O c=pb 0.0 0.0 0.0 0.0 0.0

Re: [SIESTA-L] pseudopotential for Metal-oxide surface.

Haibo, Thank you very much. Actually, I want to know. Whether the pseudopotential made for the Mg surface can be used for the MgO surface? Or else, we should generate another one for the MgO？ Because we should consider the electron transfer from Mg to O on the MgO surface. So for the Mg surface I

[SIESTA-L] pseudopotential for Metal-oxide surface.

Dear all, I want to generate pseudopotential for Metal-oxide surface such as ZnO, MgO. As we know in ZnO, MgO, metal valent state is +2, so when we generate the pseudopotential, what should we do ? minus 2 electrons? or use all the electrons? for example, Mg 1s2 2s2 2p6 3s2 should be changed to 1s

Re: [SIESTA-L] error when generate pseudopotential. rcond too small.

Dear Vozny， this is the inputfile according to one paper. pe Au, GGA, rcore=1.20 tm2 3.0 n=Au c=pbr 0.0 0.0 0.0 0.0 0.0 123 60 1.00 0.00# 4s2 52 10.00 0.00# 4p0 61 0.00 0.00# 3d

[SIESTA-L] error when generate pseudopotential. rcond too small.

Dear all, I tried to generate pseudopotential for Au according to one paper. But the result seems not so good. There is message showing " Core radius ( 2.40) outside wfn extremum ( 2.33) rcond too small: 9.448227993155600E-008 rcond too small: 9.448227993155600E-008 rcond too small: 9.448

[SIESTA-L] quick questions about checking charge density by xcrysden and rho2xsf

Dear all I want to check the charge density about the molecular adsorbed on the surface. When we use the rho2xsf , there is a lot of the choices,such like [...@linux]$ rho2xsf Specify SystemLabel (or 'siesta' if none): test Now define the grid cell for your XCrysDen plot. Note that it can be ar

[SIESTA-L] simple and basic question about frequency

Dear all, The phonon frequency can be calculated by siesta. what I want to know is the difference between the phonon frequency and vibration frequency? And siesta seems can not calculated vibration frequency of the adsorbed molecular on the surface? I am going to write a program to calculate it? H

Re: [SIESTA-L] How to construct Ultrasoft-pseudopotentials

Dear Andrei, Thank you for your suggestion. I found the lectures in the Siesta tutorials. About the pseudopotential powerpoint. there seems some detail. but unfortunately, no explanation there. Only several Data Graph, a little different to understand it. for example .PPT shows Generation Mechanics

Re: [SIESTA-L] How to construct Ultrasoft-pseudopotentials

Thank you very much. If there is no Ultrasoft pseudopotentials for siesta. Which kind of pseudopotential we usually use for the tranisition metals. It seems nobody use the potential on the siesta Homepage. On Mon, Apr 5, 2010 at 3:22 PM, wrote: > > Dear all, > > I want to construct the Ultrasoft

[SIESTA-L] How to construct Ultrasoft-pseudopotentials

Dear all, I want to construct the Ultrasoft-pseudopotentials for tranisition Metals. I read the David Vanderbilt's paper in 1990. But I can not understand it well. How to decide the cutoff radii and the electron number on each orbital? Is there anybody can give me some tips? Thank you very much. Y

Re: Re : Re : Re : [SIESTA-L] the reason i cannot use surface tab in the gdis

>> >> >> >> David "Pocket" Cornil >> PhD Student - FNRS Research Fellow >> >> Laboratory for Chemistry of Novel Materials (CMN) >> >> University of Mons >> >> 20 Place du Parc >> >> 7000 Mons >> >>

Re: Re : Re : [SIESTA-L] the reason i cannot use surface tab in the gdis

Hi，Dear David , but what's the meaning about the depth in surfaces-depths. I think the depth is for the layer of the surface.why it has two variable?

Re: Re : Re : [SIESTA-L] the reason i cannot use surface tab in the gdis

surface builder tools to > create your surface. > > Hope it's help, > > > > David "Pocket" Cornil > PhD Student - FNRS Research Fellow > > Laboratory for Chemistry of Novel Materials (CMN) > > University of Mons > > 20 Place du Parc > &

Re: Re : [SIESTA-L] the reason i cannot use surface tab in the gdis

Dear David , Thank you for your answer. You mean the Gdis can optimize structure? But it is still a little diffcult for me to understand it. can you give me some detail? It seems the software that I download is little simple than the manual. Thank you very much Fen

[SIESTA-L] the reason i cannot use surface tab in the gdis

Dear all, Is there anybody using gdis to construct surface? I tried several times but failed . I use the gdis 0.89 to construct Au(111) surface. the steps is Tools --building-edit-add atom. and then I want to use tools--building-surface ,but it didnot work and showed "your model is not 3D periodic"

[SIESTA-L] The details about constructing surface by gdis.

Dear all, One month ago, I asked which software is suitable to construct the surface. And thank you for your kind responds. I tried to use gdis, but I didnot succeed. Can you gvie me some details to construct the surface by gdis. yours, Fen

[SIESTA-L] how to cleave the surface?

Dear all, I am trying to cleave the surface by hand. but the result is different from the right one. And I still can not understand how do the cleaved surface coordinates come out. for example for the MgO surface. I think the (100) surface coordinate should be Mg(0 0 0) O (a a/2 a/2). while the cor

[SIESTA-L] Questions about the *.FC file answer given by siesta-L

Dear all, There is a subject "Problem in understanding .FC file" in Siesta-L. When somebody explained the meaning of the *.FC file, he said " the .FC file contains not just the elements of dynamical matrix, but raw values of Force/Displacement, independently for each displacement which are all d

[SIESTA-L] Re: How to explain *.FC file?phonon frequence is the same with vibration frequence when the system is molecule?

by the way the *.FC file is Force constants matrix 62.8765777 -2.4443990 -0.0010765 -30.4541102-23.0796420 -0.177 -33.0017630 26.3072340 -0.017 62.8694157 2.4497381 0.0003247 -33.0033979-26.3069681 -0.099 -30.4441874

[SIESTA-L] How to explain *.FC file?phonon frequence is the same with vibration frequence when the system is molecule?

Dear all, I am trying to get the force constant matrix of water molecule, But I cannot understand the output *.FC file well even I read the answer on the siesta-L. I think there should be 3N*3N matrix in the *.FC file. actually, there is only 54 coordination. As the siesta-L answered before, there

Re: [SIESTA-L] singlet/triplet Oxygen atom

Yes, I think you are right. But I have another question, when we do the simulation about surface, is it nesscery to fix the spin. If necessary, how can we know the electrons in the infinte system? On Thu, Feb 18, 2010 at 12:29 AM, Alexander Vozny wrote: > You mean when there is one electron, the

Re: [SIESTA-L] singlet/triplet Oxygen atom

Hi, Alexander Vozny The number of total spin is S or 2S+1 ? I always use the S(one electron 0.5) You mean when there is one electron, the number of total spin is 1 not 0.5? 2010/2/16 Alexander Vozny > you should do like this.calculate the totalspin yourself . >> FixSpin .true. >

[SIESTA-L] how to set the bandlines in fdf

Hi, all, I want to calculate the band structure and there is example such like that: BandLinesScale pi/a %block BandLines # These are comments 1 0.000 0.000 0.000 \Gamma # Begin at Gamma 50 2.000 0.000 0.000 X # 25 points from Gamma to X 20 2.000 1.000 0.000

Re: [SIESTA-L] singlet/triplet Oxygen atom

Hi’ you should do like this.calculate the totalspin yourself . FixSpin .true. TotalSpin 0.5 On Mon, Feb 15, 2010 at 4:37 PM, Rose Mary wrote: > All, > > I need to calculate the total energy of both singlet and triplet states of > an isolated oxygen atom, but I don't know how

[SIESTA-L] how to calculate the band structure?

Hi, everyone, When we do the sponon frequence, the bandlines should be block. but how to do it. Is there somebody that can give me som clue? Thank you very much Yours, Fenhong

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

Hi Thank you very much. I did a program and also tried the AtomCoorFormatOut . On Fri, Jan 29, 2010 at 2:06 PM, sonu kumar <1009uku...@gmail.com> wrote: > Hi Fen Hong, > > use-->> AtomCoorFormatOut ScaledCartesian with type of run=cg and cg > steps=0 > > regar

[SIESTA-L] How to chang the information produced by the Material Studio to the Lattice vectors?

supercell: 3 x 3 x 2 = 18 superc: Number of atoms, orbitals, and projectors:594 2808 7254 Which Lattice vector is the right one? and why the Internal auxiliary supercell is different? Thank you very much!! Fen Hong

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

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. 0.00

Re: [SIESTA-L] Posible SPAM: Why did atom's positions still changeafter blocked?

OK，thank you very much,

[SIESTA-L] Posible SPAM: Why did atom's positions still change after blocked?

Dear all, I blocked the positions from position 1 to 18. but it seems not work. inputfile: %block AtomicCoordinatesAndAtomicSpecies 0.0.2.35460760 1 1.441896790.832479500. 1 2.883793590.2.35460760 1 4.325690380.832479500.00

Re: [SIESTA-L] What is the reason causing hardly convergency?

Hi， Peter, Marcos The calculation is much better now, but did not finish now. Thank you very much. Yours, Fen

[SIESTA-L] What is the reason causing hardly convergency?

Deal all, It is Fen again. there still something wrong during my calculation. I changed the DM.MixingWeight ,DM.NumberPulay MeshCutoff ElectronicTemperature even the layer of the system etc. But all of them can not make the calcultaion converge. the bottom layer has been fixed. The input file is:

Re: Re: [SIESTA-L] How to fix the layer of the suface. By fix the atom position?

Fu， Thank you for your answer, but I donot think so, because I have run an example in the siesta, and it runs well. Maybe only when I use "routine" , a problem-specic "constr" routine should be written by users. What I want to do is fix the gold positions in the bottom three layers. But I am no

Re: [SIESTA-L] How to fix the layer of the suface. By fix the atom position?

Marcos， I changed the inputfile, it did not work well. and there is an error in outpufile " fixed: ERROR: sorry, constraint type Position not implemented yet" and a note "Harmless for Gamma calculations, except if a COHP analysis is intended" . It will take so long time to use k-points, so I pl

Re: [SIESTA-L] How to fix the layer of the suface. By fix the atom position?

This is the inputfile and there is no xyz file because it have not finished yet. NumberOfAtoms 51 NumberOfSpecies 5 %block ChemicalSpeciesLabel 1 79 Au 2 1 H 3 6 C 4 7 N 5 8 O %endblock C

[SIESTA-L] How to fix the layer of the suface. By fix the atom position?

Dear all, There are four layers in my system, I want to fix the 3 layers below. I use the "GeometryConstraints" to fix the atom position which in the 3 layer below. %block GeometryConstraints Position 1 position from 3 to 5 position from 5 to 9 position from 11 to 13 position from 15 to 17 positi

[SIESTA-L] How to set the thickness of vacuum layer by GDIS

Dear all , Is there anybody know how to set the thickness of vacuum layer by GDIS. I still cannot find the tool to construct the thickness of vacuum layer. Thank you very much.

Re: [SIESTA-L] the surface was totally changed after calculation

Heiko-san, thank you very much. I cannot understand that " choose some larger value for the axis perpendicular to the surface to simulate a surface layer" so I have to add vacuum layer to this system? Thank you very much Fen Hong

Re: [SIESTA-L] FC calculation problem:No species found!

Dear Heiko I checked the input file several time. The problem is that Number of species was not defined. We cannot trust the Example in siesta package sometime. Now everything is ok. On Fri, Jan 15, 2010 at 3:52 PM, Heiko Dumlich wrote: > Dear Fen Hong, > > maybe your "SystemLab

[SIESTA-L] FC calculation problem:No species found!

Dear all, I am trying to calculate the vibration frequence. This is an example in siesta 3.0 package(siesta-3.0-b/Util/Vibra/Examples/). Vibra has been compiled by "make" and I also put the pseudopotential file Si.psf in the same diectory (siesta-3.0-b/Util/Vibra/Examples/). but it did not work