Re: [SIESTA-L] TranSiesta

I donot think it is wise to advertise a stupid black box . On Mon, Jun 29, 2009 at 8:51 PM, Markus Kaukonen wrote: > Dear All, > > I disagree with Dr. Torres: > in case Siesta is not having some method built in it is useful for > users to know in which codes the desired option is present. > > Ope

Re: [SIESTA-L] Error in compiling SIESTA

ld: cannot find libmkl_intel_lp64.a please notice this information. you should set proper path for libmkl_intel_lp64.a. On Sat, Dec 27, 2008 at 2:33 AM, Amirhasan Nourbakhsh wrote: > Dear all, > > I tried to compile siesta on my PC (intel(R) Core2Duo,Red Hat,Intel > Fortran 11), but I got the fo

Re: [SIESTA-L] help about rho2xsf!!!

do you ever try to click "Tools" in the panel ? On Wed, Oct 29, 2008 at 10:29 PM, zhiyong wang <[EMAIL PROTECTED]>wrote: > Dear all siesta users: > >I have compiled the rho2xsf and Xcrysden successfully,and I use > the rho2xsf to transform the file.RHO to file.XSF format,it looks lik

Re: [SIESTA-L] Charged molecule adsorbed onto a surface

I donot think we can deal such situation with periodic cell scheme. of coz, you can change the electrons of system, but you cannot 'localize' extra electrons at certain sub-part of system... On Thu, Apr 24, 2008 at 9:48 PM, Roberto Sapiens <[EMAIL PROTECTED]> wrote: > Hi, everybody: > > I'd li

Re: [SIESTA-L] Van Der Waals

Thank you very much, dear Steven and Macros ! On Fri, Apr 4, 2008 at 6:48 PM, Marcos Verissimo Alves < [EMAIL PROTECTED]> wrote: > To add to this thread: there is an Europhysics Letters on the subject, > > J. C. Charlier, X. Gonze and J.-P. Michenaud, "Graphite interplanar > bonding: electronic d

Re: [SIESTA-L] Posible SPAM: How to calculate the interlayer inter actions of graphite using SIESTA?

as i as i know, LDA functional is mostly used to relax interlayer geometry, especially for graphite system ... i donot know why, some guy told me that it is accidentally proper to handle vdW interactions.. if you need, i can list some related refs to you. On Fri, Apr 4, 2008 at 8:11 PM, Ren Hao

Re: [SIESTA-L] Mailing list archives

should we subscribe to it again ? Best On Wed, Apr 2, 2008 at 12:47 PM, Eduardo Anglada <[EMAIL PROTECTED]> wrote: > Dear Users of Siesta, > > There is a new interface to the archives of this mailing list: > > http://www.mail-archive.com/siesta-l@listserv.uam.es/ > > It's much more easier to us

Re: [SIESTA-L] MD.VariableCell with slabs and chains

I think variable cell calculation even is a challenge for bulk system calculations. On Wed, Mar 19, 2008 at 3:31 PM, Roberto Sapiens <[EMAIL PROTECTED]> wrote: > Hi everybody: > > is MD.VariableCell also suitble for chains and slabs, or just for bulk > systems? > > []s, > > Roberto > -- Hai-P

Re: [SIESTA-L] mulliken Qtot

you should have used smearing function for accelerating scf calculation On Fri, Mar 14, 2008 at 4:21 PM, Pablo Denis <[EMAIL PROTECTED]> wrote: > Dear Siesta users, > > I have a question about mulliken Qtot. I made > this question about one year go but I still don´t f

Re: [SIESTA-L]

Dear Reza, of coz, siesta can give your PDOS and LDOS you want. first, you should set up data block for dos information in you siesta input %block ProjectedDensityOfStates -20 10 0.1 300eV %endblock ProjectedDensityOfStates please refer to userguide for more information you need. Hope help

Re: [SIESTA-L] pseudopotential for Ga and As

Dear Cherry , you can figure out from url below http://lorax.chem.upenn.edu/Research/psp_lda.html as i said before, opium package can easily generate psps for siesta with psf format. On Nov 30, 2007 3:27 PM, Cherry Y. Yates <[EMAIL PROTECTED]> wrote: > Please send them to me if you happen to h

Re: [SIESTA-L] Ti Pseudopotential

Haven, CT06520 > > > - Original Message - > From: "lan haiping" <[EMAIL PROTECTED]> > To: > Sent: Saturday, November 24, 2007 3:15 AM > Subject: Re: [SIESTA-L] Ti Pseudopotential > > > > you can use Opium package to generate PP f

Re: [SIESTA-L] Ti Pseudopotential

you can use Opium package to generate PP for siesta, just using the input file supplied at http://lorax.chem.upenn.edu/Research/psp_gga.html#Ti2. good luck On Nov 24, 2007 3:20 PM, M.Sairam Swaroop <[EMAIL PROTECTED]> wrote: > Dear Siesta Users > > I would be glad if someone could share a GGA fl

Re: [SIESTA-L]

Dear kou you can look through the user guide , all details are given there. for your this problem, you can use keywords SpinPolarized DM.InitSpinAF DM.InitSpin to control your calculation。 Bests Hai-Ping On 10/30/07, 寇良志 <[EMAIL PROTECTED]> wrote: > > Hello,everyone > I'm trying to study magneti

Re: [SIESTA-L] K mesh

dear john you should make sure that your nanotube system is periodic along z-direction. regards, On 10/2/07, John Appleton <[EMAIL PROTECTED]> wrote: > > Dear users, > I wish to perform SIESTA calculations on nanotubes. > All my previous SIESTA calculations have been > gamma point calculations. N

Re: [SIESTA-L] gold_surface

Dear Cornil i have done similar work on wf of cnt with siesta several months ago. i found that the value is sensitive to settings of PAO. so, i recommend you can try to tune these related parameters, such as EnergyShift, SplitNorm et cl. hope help Regards, Hai-Ping On 9/19/07, cornil david <

[SIESTA-L] about piezoelectric properties calculations

Dear All, I want to examine zinc oxides' piezoelectric properties with siesta , would you please recommend some references or technique details to me ? Regards, H.P -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 [EMAIL PROTECTED], [EMAIL PROTECTED]

[SIESTA-L] how to do antiferromagnetic calculation ?

Dear All, i want to do a test on antiferromagnetic properties of Fe FCC structure. Would you please give me some hints how to set input to initiate an antiferromagnetic calculation ? Regards, H.P -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 [EMAIL PROTECTED]

[SIESTA-L] How to handle this warning ?

Dear All, I am doing test calculation on Co-FCC structure, and want to examine the PP's quality . after my calculation , the siesta gave these warnings following : "KBproj: WARNING: KB projector does not decay to zero KBproj: WARNING: parameter Rmax in routine KBgen should be increased KBproj: W

Re: [SIESTA-L] Bi pseudopotential error

Dear Swaroop Would you please show the basis used with this PP ? I thought your problem may be related with your basis set .. Regards, H.P On 6/6/07, M.Sairam Swaroop <[EMAIL PROTECTED]> wrote: Dear Siesta Users We are facing a seriuos problem with the generation of pseudopotential for Bi

Re: [SIESTA-L] Pseudopotential for Fe and Bi

Dear Swaroop try this http://www.tddft.org/programs/octopus/pseudo.php On 6/3/07, M.Sairam Swaroop <[EMAIL PROTECTED]> wrote: Hi all Could someone share pseudopotentials (LDA flavor) for Bi(Bismuth) and Fe. Thanks Swaroop -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalor

Re: [SIESTA-L] construct basis set

Dear Jess, for semicore PP, you should explicitly input PAO.Basis. You can find example in siesta web, as far as i know. For example, there is Ti 's PP and PAO.Basis in semicore situation. Regards, hai-ping On 1/27/07, Jess Kondor <[EMAIL PROTECTED]> wrote: Dear all, I created a pseudopo

Re: [SIESTA-L] Total Potential

hi, the unit is V. regards, hai-ping On 12/22/06, Thiagobm <[EMAIL PROTECTED]> wrote: Dears users, In which unit is gave the total potential written by SIESTA? Thank you, Thiago B. Martins -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871

Re: [SIESTA-L] problem for siesta-2.0 compilation.

AGS) atom.f # dfscf.o: $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) dfscf.f # electrostatic.o: $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) electrostatic.f otherwise the forces on the atoms will not be evaluated properly. Regards, Phil. lan haiping a écrit : > Dear All, > > I tried to compile sie

Re: [SIESTA-L] calculation failure of siesta-2.0

Thank you, Daniel. The program was crashed with error of SIGSEGV.. I donot know how to fix this problem :(, it troubles me for a long time. Regards, Hai-Ping On 12/19/06, J. Daniel Prades Garcia <[EMAIL PROTECTED]> wrote: lan haiping wrote: > Dear All, > > I tried to figure

[SIESTA-L] calculation failure of siesta-2.0

Dear All, I tried to figure out calculation failure of siesta-2.0 in AMD-x86-64/Pgi6.0 environment. and found siesta ceased almost at calling subroutine InitMesh. Could you please give me some sugguest fixing such calculation failuer ? Regards, Hai-Ping -- Hai-Ping Lan Department of Elect

[SIESTA-L] problem for siesta-2.0 compilation.

Dear All, I tried to compile siesta-2.0 with pgi 6.0 compilor under x86-64 environment. With arch.make file that tested for siesta-1.31, i can compile the siesta-2.0 package without any complain. But siesta-2.0 cannot finish any computation even for simple h2o energy caclulation. All error infor

Re: [SIESTA-L] Why it is so hard to converge with 32 atom unit cell.

you can tune parameters : DM.MixingWeight and DM.NumberPulay On 12/5/06, siesta88 <[EMAIL PROTECTED]> wrote: Dear SIESTA users: I used dzp atomic basis,160 ry meshcutoff ,30 Bohr kgrid cutoff to calculate FePt system(see the pictures of my unit cell in attachment), however, it seems to take fo

Re: [SIESTA-L] GGA pseudopotential for Cu

hi , psf below is captured from octopus .. you should do some tests on it .. regards hai-ping ~~!! pg Copper tm2 0.00 n=Cu c=car 0.0 0.0 0.0 0.0 0.0 0.0 54 40 1.00 0.00 41 0.00 0.0

Re: [SIESTA-L] Pseudopotential help

hi atom routine is sensitive to pp file format.. Try to start with a correct format file ,and modify its parameters.. hope help regards. hai-ping On 11/7/06, Saswata Bhattacharya <[EMAIL PROTECTED]> wrote: Dear all, i am trying to run atom program for Boron Pseudopotential and my .tm2.inp

Re: [SIESTA-L] All electron calculations with SIESTA

atom in Pseudo can do full potential calculation for single atom.. regards, hai-ping On 10/30/06, J.Daniel Prades <[EMAIL PROTECTED]> wrote: Dear SIESTA users, I wonder if, additionally to the calculations based on pseudo-potentials, is it possible to perform all electron calculations

Re: [SIESTA-L] About unoccupied channels in the basis set

Hi Marcos, you could define pao-basis with keywords PAO.Basis . in this block, you may include some shells you like to define regards, hai-ping On 10/27/06, Marcos Verissimo Alves <[EMAIL PROTECTED]> wrote: Dear all, I have a doubt about the inclusion of unoccupied channels in the basis set,

Re: [SIESTA-L] Ask for pseudopotential of Si

Hi, you can download PP for Si from siesta web.. there are several examples regards, hai-ping On 10/19/06, 杨福华 <[EMAIL PROTECTED]> wrote: Dear everyone: I am doing some calculation about Si supercell, I want to use the norm-conserving pseudopotential of Si generated by this met

Re: [SIESTA-L] about the transiesta

Dear Jian, as far as i know, transiesta donot have academic license. it is a commercial software.. you could google it, and try to find more about it. Regards, hai-ping On 10/13/06, Jian ZHOU <[EMAIL PROTECTED]> wrote: Dear all, Does anyone know how to obtain a license of the academic tra

Re: [SIESTA-L] NaN error with parallel version of Siesta 2.0

Dear Derek, try to tune DM.MixingWeight and DM.NumberPulay. Regards, Hai-Ping On 10/4/06, Derek A. Stewart <[EMAIL PROTECTED]> wrote: Hi all, I have been trying to get the parallel version of Siesta 2.0 to run with the intel compilers (version 8.1, MKL math libraries) and lam-mpi (7.1.1)

Re: [SIESTA-L] siesta compilation problem

hi, john. I donot have experience for compilation in sgi machines. Only i can say that your errors are related to mathlib path. you should give proper path for math lib linking. regards, hai-ping On 9/26/06, John B. Baba <[EMAIL PROTECTED]> wrote: Hi all: Thanks lan and Marcos replay,

Re: [SIESTA-L] siesta compilation problem

hi, if you wanna use netcdf, you should define the lib for netcdf properly. it is not necessary to use netcdf to compile parallel version of siesta. regards, hai-ping On 9/22/06, John B. Baba <[EMAIL PROTECTED]> wrote: Hi all: I also try to compile siesta1.3 parallel using mpi and f90 in s

Re: [SIESTA-L] parallel compilation error

you neednot use netcdf for compilation. On 9/22/06, Tao K <[EMAIL PROTECTED]> wrote: Dear Siesta user, These days I try to compile parallel Siesta-2.0 on a AMD-Opteron cluster, but I always fail to do this and encounter a problem: fortcom: Error: basis_io.F, line 55: Error in opening the Li

Re: [SIESTA-L] pseudopotential problem?

hi, the input file of atm routine should be strict in format .. so , you can modify some good input files , and set parameters for C element hope help regards, hai-ping On 9/1/06, Chun Li <[EMAIL PROTECTED]> wrote: Dear all: I need help eagerly. I encouter a problem after generating the

Re: [SIESTA-L] Gold band structure

Dear Oleksandr, Would you have PP-basis of other metals ? Just like Pd/Pt etc.. Thanks Regards, hai-ping On 8/30/06, Oleksandr Voznyy <[EMAIL PROTECTED]> wrote: Hi Salvador, first of all pseudo for gold should be relativistic - it's a heavy atom and relativistic effects change significa

Re: [SIESTA-L] about Fermi level!

Hi, absolute Fermi level is not of physical meaning ... regards, On 8/29/06, Mingsu Si <[EMAIL PROTECTED]> wrote: Dear all, How to understand that the Fermi level is positive? Thank you! Mingsu Si

Re: [SIESTA-L] simplex

Hi, you can find such code in Numerical Recipes.. Regards, H.P On 8/22/06, eb na <[EMAIL PROTECTED]> wrote: Dear Siesta users, can anybody help me to get a simplex code to optimze the basis for siesta? Best regards, E. Nadimi -- Was Sie schon immer wissen wol

Re: [SIESTA-L] Problem encounted when using basis type split

%endBlock PAO.Basis hope help~~ Regards, Hai-Ping On 7/18/06, 王秦镜 <[EMAIL PROTECTED]> wrote: Pt - Original Message - *From:* lan haiping <[EMAIL PROTECTED]> *To:* SIESTA-L@listserv.uam.es *Sent:* Tuesday, July 18, 2006 2:52 PM *Subject:* Re: [SIESTA-L] Problem encounte

Re: [SIESTA-L] Relaxation factors

of coz , tests for different meshcutoff for molecule are enough.. On 7/18/06, Michael Shin <[EMAIL PROTECTED]> wrote: Hello I am relaxing the atomic cordinates of Molecules usig CG. I converged the calculations for different CuoffMesh and I think I dont have to convege for K-points bcos I a

Re: [SIESTA-L] Problem encounted when using basis type split

what element you calculated ? On 7/18/06, 王秦镜 <[EMAIL PROTECTED]> wrote: Hi everyone When I use the flags as follows: PAO.BasisTypesplit PAO.BasisSizeDZP the program stopped with information as follows: POLgen: Polarization orbital for state 6s POLARIZATION: Iteration to find th

Re: [SIESTA-L] problem during excecution

Dear Vikas, you should export LD_LIBRARY_PATH for the libs related intel-compiler On 7/15/06, vikas sharma <[EMAIL PROTECTED]> wrote: I am trying to run the SIESTA program on *SuSe 9.0,* using *intel fortran compiler*. but during the excetiution i am getting the error message, " error while

Re: [SIESTA-L] About VariableCell CG calculation

Dear Marcos, Thank you . I just terminated the running , because the lattice vectors are longer about 1 Ang than experimental values. The meshcutoff is enough, because most published results on TM-oxide calculated by siesta are set meschcutoff from 150 Ry to 200 Ry. The kgrid setting was a

Re: [SIESTA-L] About VariableCell CG calculation

Hi, The kgrid_Monkhorst_Pack setting is according to Monkhorst-Pack scheme for k-grids sampling. You can refer to this original paper. Of coz, the kgrid-setting will affect results greatly. Genenerally, the more grids, the more k points are sampling in the BZ. We should do some tests on this gr

[SIESTA-L] About VariableCell CG calculation

Hi ,All . I am trying to do TiO2-anatase bulk calculation, with the pseudopotentials and basis-sets from siesta web. I found that i could not successfully finish the variable cell calculation with proper lattice parameters. The atomic coordinates and lattice vectors are taken from MaterialStudi

Re: [SIESTA-L] Confusion with output

Thank you ! I just found my wrong typing for it after submitting this message. Regards, hai-ping On 7/13/06, Andrei Postnikov <[EMAIL PROTECTED]> wrote: On Thu, 13 Jul 2006, lan haiping wrote: | Hi, All! | | I have a confusion with siesta's output . | I have set the AtomicCoordi

[SIESTA-L] Confusion with output

Hi, All! I have a confusion with siesta's output . I have set the AtomicCoordinatesFormat to* Ang*, But i found the atomic coordinates in output with the same values in *Bohr . * ** Part of output is below, would you please help me ? regards, Hai-Ping *Input :* ** *AtomiCoordinatesFormat Ang %

[SIESTA-L] Not converged ?

Hi , All, I just run a cell-variable CG calculation on Pd bulk , and found some stranges . Following is my input file : *SystemName Pd SystemLabel Pd-rlxDZ* *NumberOfAtoms4* *NumberOfSpecies 1 %block ChemicalSpeciesLabel 1 46 Pd %endblock ChemicalSpeciesLabel PAO.Ener

Re: [SIESTA-L] plrho compilation png type error

yes , this is the error related to lib link . On 6/29/06, Orlin Blajiev <[EMAIL PROTECTED]> wrote: Hi, I will appreciate any hints about the error appearing during plrho compilation. Is this some library missing? /usr/lib/libpgplot.so: undefined reference to `png_set_text' /usr/lib/libpgplot

Re: [SIESTA-L] Problems about Diagonalization termination in Siesta-2.0 & Siesta-1.3

Dear Javier Thanks for your suggestion. I have tried this setting in my calculation , but failed. it still gives me the same error information . Regards, Hai-Ping On 6/26/06, Javier Junquera <[EMAIL PROTECTED]> wrote: Dear lan: In Siesta 2.0, try to switch the Divide And Conqu

[SIESTA-L] Where is the murna routine?

Dear developers : In siesta-2.0 , Tutorial/Bases/Si_bulk , there are 2 scripts , just as fit.sh and plot.sh. this is the content of fit.sh *#!/bin/sh* *rm -f fit.dat cat > fit.dat <> fit.dat murna fit cat fit.mout * Since i cannot find the routine murna in Src or Util directory, i would l

[SIESTA-L] pseudopential and basis for Pd

Hi, Does anyone have a pseudopential for Pd , and related basis ? Using the default basis , my calculation for Pd bulk run into diagonalization error, and i would like to try another basis and pseudopotential. Thanks Regards, Hai-Ping

[SIESTA-L] Problems about Diagonalization termination in Siesta-2.0 & Siesta-1.3

Dear developers : I have come to errors in performing Pt-bulk CG-relaxation calculation both in siesta-2.0 and 1.3 . Would you please give me some hints ? The error occured in first CG step , and the code gave this information : * Error in Cholesky factorisation in cdiag St

[SIESTA-L] How to dwell with this error ?

Dear All, I just came to an error below, would you please give me some hints about it ? The leading minor of order11 of B is not positive definite. The factorization of B could not be completed and no eigenvalues or eigenvectors were computed. Terminating due to failed diagonalis

[SIESTA-L] How to deal with memory corruption in parall-running

Dear All, I have a problem related to memory corruption in parall-running . My workstation is SMP AMD-Operon 248 and RHEL AS 4.0 with 2.6.9-34.ELsmpkernel version, while glibc is x86_64-redhat-linux/3.4.3 . When i just parallelly run a simple job ,just like Examples/Fe, it gave memor

[SIESTA-L] Question about SIESTA-ART nouveau

Dear developers, I would like to ask whether the SIESTA-ART nouveau method for calculating diffusion pathway is implemented in SIESTA-2.0 ? This method was described in PHYSICAL REVIEW B 70, 205202 . Regards, H.P.