Re: [SIESTA-L]

/~luxu == Eduardo Anglada writes: Hi, Could you please post your results and the input fdf? The energy should converge. Best Eduardo On 01/11/2008, at 15:23, Xu Lu wrote: Dear all : I have a problem in calculating the energy of single atom. The energy

Re: [SIESTA-L] Crazy SCF with vanadium

Could you please post your V pseudo? The mesh cutoff doesn't vary the scf, it only controls the rippling of energy/forces. This rippling is due to the FFT aliasing of those magnitudes (orbs^2,neutral atom potential, core charge for non linear core corrections) which are projected into the

Re: [SIESTA-L] Bulk cohesion energy

Hi, At the beginning of each SIESTA run, during the generation of the atomic orbitals, the number of basis functions for each species is written. Best Eduardo On 03/11/2008, at 21:05, Roberto Veiga wrote: Where in the output can I find the number of basis functions? Roberto From: Oleksandr

Re: [SIESTA-L] Bulk cohesion energy

do I obtain the total number of basis functions for a condensed system? Should I take into account more than the atoms explicitly defined in my input? Roberto From: Eduardo Anglada [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Tuesday, November 4, 2008 9:45:34 AM Subject: Re: [SIESTA-L

Re: [SIESTA-L]

Hi, Could you please post your results and the input fdf? The energy should converge. Best Eduardo On 01/11/2008, at 15:23, Xu Lu wrote: Dear all : I have a problem in calculating the energy of single atom. The energy will drop linearly with respect to decreasing of energy shift. It

Re: [SIESTA-L] Plrho compilation problem

*** I'm fairly confused now which compiler to use for using Siesta and Utils. Note: Siesta works fine now :) Thanks, Regards, From: Eduardo Anglada [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Thursday, October 30, 2008 9:55:07 AM Subject: Re: [SIESTA-L

Re: [SIESTA-L] Multigrig solver for Poisson Equation

Hi, As far as I know It is not being distributed. Best, Eduardo On 29/10/2008, at 12:48, José Eduardo Padilha de Sousa wrote: Hi All. In a recent article about SIESTA (J. Phys.: Condens. Matter 20 (2008) 064208), I read that a multigrid solver for the Poisson equation on the grid has been

Re: [SIESTA-L] plstm problem

Hi, Try with: a.out input Best, Eduardo On 30/10/2008, at 5:18, Руслан Жачук wrote: Dear SIESTA users, I am using OpenSUSE Linux 10.3 and installed following packages to compile SIESTA utilities: 1) gcc-fortran (4.2) //The system GNU Compiler 2) gcc42-fortran (4.2.1_20070724) //The GNU

Re: [SIESTA-L] Plrho compilation problem

Hello You have to use the same compiler for the utils and for siesta. Could you please post the error message? Best, Eduardo On 29/10/2008, at 18:17, Johnny Dry wrote: Hello Siesta users, I'm using: * Mandriva Linux 2008 * g95 compiler * Siesta 2.0.1 I've compiled these packages: * Siesta

Re: [SIESTA-L] Qtot convergence pb is back

Hola Roberto, Then the problem is that your compiler does buffering I/O. As the buffer isn't full there is no flush of the communication channel and the slave siesta waits forever. Almost all the compilers have an option which turns off the buffering. Best, Eduardo On 22/10/2008, at 12:50,

Re: [SIESTA-L] Pseudo_for_C

Dear Alexandre, Why do you fix the radius of all the channels to the same value? In principle the matching radius is different for each angular momentum channel. Best regards, Eduardo On 15/10/2008, at 16:00, Alexandre Lebon wrote: Dear Siesta users, I am meeting some difficulty at

Re: [SIESTA-L] Gap in ZnO

On 11/10/2008, at 9:52, Subhra Kulshrestha wrote: Dear users, I am also facing the same problem in computing the band structure of f-band materials. They are semiconducting but the band structure calculated from LDA, LSDA, GGA, GGA+spin gives metallic behaviour. I want to get it

Re: [SIESTA-L] pair correlation function and self diffusion

Dear Karim, It is possible, but you have to construct the program yourself. Best, Eduardo On 11/10/2008, at 14:44, karim rezouali wrote: Dear SIESTA users, Is it possible to calculate the following parameters using the SIESTA code? 1. Pair correlation function 2. the self diffusion

Re: [SIESTA-L] the use of plrho!

Hi, You have to compile plrho exactly (with the same compiler and options) the same as the siesta you are going to use. If you mix compilers and/or options it won't work. Best, Eduardo On 07/10/2008, at 14:59, zhiyong wang wrote: hi,all siesta users: I have compiled the plrho in my

Re: [SIESTA-L] LDOS and broadening

Hi, David is correct, you have to decrease the electronic temperature. If you encounter any difficulties send me a message. Best regards, Eduardo On 03/10/2008, at 19:40, David Strubbe wrote: I think the LDOS is broadened by the electronic temperature, so maybe you have to decrease that.

Re: [SIESTA-L] Problem with optimization using variable cell]

Hi Arun, This problem happens from time to time. It's quite frustrating because I haven't been able to reproduce it, so I don't have any clue. What happens if you restart? Does the output include the cell vectors of the last step? Maybe they can be found in the XV file. The crash happens during

Re: [SIESTA-L] Question about finding barrier height

Hi Kamaram! Do you need so many planes? The calculation is going to be very long! If you need the LDOS you should include the following option in the input fdf: %block LocalDensityOfStates Emin Emax units %endblock LocalDensityOfStates The Emin and Emax (Emin Emax) specify the

Re: [SIESTA-L] Can anyone solve the problem on downloading SIESTA?

Dear Adrian, We are really sorry, we're trying to solve this issue. If you can't wait I will send it to you (or anybody else). Best regards, Eduardo On 30/09/2008, at 5:24, Adrain Zhou wrote: Dear all, I can not download SIESTA code from

Re: [SIESTA-L] mpi error with siesta 2.0.x using intel compilers on infiniband

Hi, Are you able to run (successfully) scalapack and blacs tests? Maybe the problem has nothing to do with siesta, it looks like a communication problem. Regards, Eduardo On 23/09/2008, at 4:30, M Bharat Kumar wrote: Hello All, When trying to run simulations using siesta on our new cluster,

Re: [SIESTA-L] Queries about reliability of SIESTA under LDA

Dear Nidhi, On 24/09/2008, at 8:50, Nidhi Sharma wrote: Dear Users, I have computed the high pressure properties and electronic structure calculations of a semiconducting heavy earth compounds with LDA and non-relativistic, alongwith polarization orbitals : perturbative polarization.

Re: [SIESTA-L] simulation of metal alloy liquid

Dear Chol-Jun Yu, Siesta can do this kind of molecular dynamics simulations. In the input fdf file you should include the following options: WriteMDhistory WriteMDXmol At the end of the simulation there will be two output files: SystemLabel.MD - contains positions and velocities at every time

Re: [SIESTA-L] mpi error with siesta 2.0.x using intel compilers oninfiniband

On 02/10/2008, at 17:58, Bharat wrote: Hi Eduardo, Thanks. scalapack and blacs work fine. Anyhow I figured its a problem with mvapich2. With openmpi, I could run the problematic input files successfully. Great!! On Thu, 02 Oct 2008 01:52:42 -0600, Eduardo Anglada [EMAIL PROTECTED

Re: [SIESTA-L] Hybrid functional calcualtion

Hi, I'm really sorry but the PBE0 functional is not implemented in SIESTA. Regards, Eduardo On 01/08/2008, at 7:54, Adrain Zhou wrote: Dear all, Is there anybody has experience with hybrid functional (PBE0) calcualtion? Could you please tell me how is the performance? Do I use only PBE atom

Re: [SIESTA-L] Help with compilation error

Hi Tom, There is a problem in Makefile or arch.make files, the make program doesn't know how to compile a given file, and it call the c compiler without any input. Regards, Eduardo On 10/08/2008, at 4:08, Thomas Sadowski wrote: Hello all, I am attempting to compile parallel siesta on an

Re: [SIESTA-L] Strange mpi problem

Hi Lakee, I think you have a problem with you openmpi setup, it tries to use infiniband, but it can't find any network cards so it uses standard ethernet. What I recommend is: 1) Check the tests and examples of openmpi. 2) Compile and test Blacs. If the test fail SIESTA will fail, so don't

Re: [SIESTA-L] Blue Gene arch.make

Hi, I've asked a person who runs siesta in Blue Gene and this is her arch.make. She had to compile scalapack by hand. SIESTA_ARCH=XLF 32bits PARALLEL # FC= mpixlf90 #xlf90_r # FFLAGS_DEBUG= -g FFLAGS= -O5 -qarch=440d -qtune=440 COMP_LIBS= RANLIB=echo # NETCDF_LIBS= NETCDF_INTERFACE=

Re: [SIESTA-L] Work function of Si

Hi, Please take a look at this previous posting by Javier Junquera. He has written a nice review about the subject http://www.mail-archive.com/siesta-l@listserv.uam.es/msg00627.html Best regards, Eduardo On 18/07/2008, at 20:34, zubaer wrote: Hi, I wanted to calculate the workfunction

Re: [SIESTA-L] Electric field

of the zigzag profile? Luis From: Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta [mailto:[EMAIL PROTECTED] On Behalf Of Eduardo Anglada Sent: Tuesday, July 15, 2008 7:35 AM To: SIESTA-L@listserv.uam.es Subject: Re: [SIESTA-L] Electric field Hello Luis, Siesta solves

Re: [SIESTA-L] Electric field

Hello Luis, Siesta solves the Poisson equation using ffts, so the zig-zag potential due the electric field is allowed in the directions where there is vacuum. But siesta doesn't introduce a fictitious dipole charge (as far as I know). Maybe if you change the cell geometry and the values of

Re: [SIESTA-L] Ag pseudopotential

Hi, You can find the translation of abinit's pseudos into siesta psf format here: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/periodictable-intro.html Regards, Eduardo On 13/07/2008, at 14:56, Tafoughalt Mohand Akli wrote: Dear SIESTA users, I need a pseudopotential

Re: [SIESTA-L] Memory problem when running Siesta in parallel

. Thanks -Kam Eduardo Anglada [EMAIL PROTECTED] wrote: Hi, This error also happens with intel fortran compiler. Kamaram, could you send me a copy of the fdf and pseudos? Also I need the compilation options you used. Regards, Eduardo On 27/06/2008, at 19:18, Marcos Verissimo Alves wrote: Hm

Re: [SIESTA-L] Cobalt

written / Lei ha scritto / Você escreveu... Eduardo Anglada Hi, That's the problem, there is no ultimate systematic scheme. My recommendation: Start optimizing the energyshift parameter. Once the energy is converged with respect to this parameter then you can optimize the splitnorm of the multiple

Re: [SIESTA-L] Memory problem when running Siesta in parallel

Hi, This error also happens with intel fortran compiler. Kamaram, could you send me a copy of the fdf and pseudos? Also I need the compilation options you used. Regards, Eduardo On 27/06/2008, at 19:18, Marcos Verissimo Alves wrote: Hm, this seems to be a complicated error. Googling malloc():

Re: [SIESTA-L] SIC

Dear Ebrahim, I'm really sorry but it is not distributed. Regards, Eduardo On 06/06/2008, at 13:09, eb na wrote: Dear Siesta community, could anybody tell me if the SIC correction which has been implemented and reported in PRB 75, 045101, is already implemented in any Siesta distributed

Re: [SIESTA-L] EHarris NaN error

Hi, Try to reduce the compilers optimization level, it seems to be very aggressive. Regards, Eduardo On 05/06/2008, at 11:14, Sharat Chandra wrote: Hi I am using version 2.01 with all the updates and I am trying to run CG minimization on a large system with 720 atoms (Fe, Ti and C) a

Re: [SIESTA-L] WARNING: Qtot

Dear Reza, There is a bug in siesta, it can't calculate a system with only 1 orbital ... Regards, Eduardo On 04/06/2008, at 2:28, reza behnam wrote: Dear Edan, Thank you for your advises. According to Eduardo`s and your advises I set the PAO.Basis as DZP and it worked. But why?just

Re: [SIESTA-L] compile error of parallel version

you give me again comments? With kind regards, Chol-Jun Eduardo Anglada wrote: Hi, You compiled blacs and scalapack with gfortran or g77, while siesta was compiled with ifort (intel fortran). You shouldn't mix compilers. Regards, Eduardo On 28/05/2008, at 9:11, Chol-Jun Yu wrote: Hello

Re: [SIESTA-L] ghost atoms: labels

Dear Andrei, Siesta uses the species number in order to identify the different species, there is no subrutine which lets you identify a species by it's label so it's quite safe to use the same label for several species. But it can be very error prone, so I recommend to have different labels for

Re: [SIESTA-L] negative value for MESH

Dear Swaroop, Which are the values of the mesh in the previous CG steps? Are they very different? Maybe we can guess what is going on. Regards, Eduardo On 23/05/2008, at 14:24, M.Sairam Swaroop wrote: Dear Eduardo We have compiled siesta with a 64 bit compiler and we have allowed for a

Re: [SIESTA-L] negative value for MESH

Clearly there is something wrong going on. Can you send me (privately) the hole output (including the output files with coordinates and cell) Best, Eduardo On 23/05/2008, at 18:26, M.Sairam Swaroop wrote: Dear Eduardo After you mentioned i noticed tha the mesh does not change ... i have

Re: [SIESTA-L] Total energy vs. Energy Shift convergence

Dear Roberto, Maybe what you are seeing is the rippling of the energy/forces due to the aliasing (wrap around errors) of the fft. The orbitals (squared) and neutral atom potential are projected into the grid so if you change them this error can introduce noise in the convergence of the total

Re: [SIESTA-L] Regarding some error in optical properties

On 21/05/2008, at 12:53, Subhra Kulshrestha wrote: Dear Users, I have computed the optical properties of Si by using two program input.f and optical.f in the directory siesta-2.0.1/Util/Optical and the program is successfully run for Si but as I run the calculation for LaAs the file

Re: [SIESTA-L] Wrong Results with pathscale compiler

Dear Philipp, Currently we are working with pathscale for a solution of your problem. Once we know how to compile siesta with the latest version of the pathscale compilers I will provide the arch.make. For the other versions of pathscale compiler use the arch.make provided by Pablo Aguado. Best

Re: [SIESTA-L] Convergence test for the mesh cut-off and k-point

Hi, For the mesh cutoff change the meshcutoff variable from the default of 100 Ry to 500 in steps of 100 Ry, if the energy converges (also take a look at the forces) you are done with the grid. If it is not converged you should continue increasing the mesh cutoff. If you reach a very huge

Re: [SIESTA-L] determining Fermi energy

I'm sorry, I should have answered before! I think that your pseudocode is right. That is what siesta does in order to obtain the position of the Fermi level. Best regards, Eduardo On 02/05/2008, at 20:03, David Strubbe wrote: Ebrahim, No I never received any response, but I recently

Re: [SIESTA-L] Overestimation of optimized lattice constant for SmTe

On 03/05/2008, at 12:39, Nidhi Sharma wrote: Hi to all, I am trying to compute the energy for different lattice constant to get the E vs V graph (in B1 phase of Smte using LDA). For this I have selected the range from 5.5 to 7.5 Ang in steps of 0.05. After Murnaghan fit optimize

Re: [SIESTA-L] multiple-zeta

Hi, If you are using the latest version of siesta you should use another diagonalization scheme. Try changing the following options (they are fdf booleans: .true. or .false. )in your fdf: Diag.AllInOne(default false, change to true) DivideConquer (default true, change to false)

Re: [SIESTA-L] cell optimization with fixed angles

Hi, Yes it is possible, but you should write your own constraint subroutine. Take a look at the example in Src/constr.f Regards Eduardo On 06/05/2008, at 10:52, eb na wrote: Hello dear Siesta community, How can I optimize the atomic coordinates and cell sizes while keeping the cell

Re: [SIESTA-L] Pseudopotential and basis for Co

Hi Ali, In the webpage there are LDA GGA pseudos, but I have no basis sets. http://www.uam.es/departamentos/ciencias/fismateriac/siesta/periodictable-intro.html Regards, Eduardo

Re: [SIESTA-L] Bromine pseudo

Hi Roberto, I attach the output of Bromine pseudo generation using the Fritz Habber Institute (fhi) code. The input was taken from Abinit's LDA/GGA databases. The translation of the output of fhi to siesta leads to ghost states (siesta uses a different definition of the local part of the

Re: [SIESTA-L] Converging a cluster of Ni Atoms

Hi, Why are you using the split gauss option? Have you checked the resulting gaussians? Do they decay to zero? Regarding the convergence, if the Harris Energy is converged, you could try to stop the calculation and restart it (reading the coordinates and density matrix). It many

Re: [SIESTA-L] Is there a psf for La

Hi! This message is not related to the pseudo of La! So please use a new subject line Can we see the arch.make? It contains all the compiler, libraries related stuff Regards, Eduardo On 10/04/2008, at 14:13, Pablo A. Denis wrote: Dear Siesta user, I

Re: [SIESTA-L] Valence configuration of samarium

is possible although it contains 10 electrons. This is a misprint in the head line of the Te pseudo. It was generated with 4d10 in the core and 5d as valence states. (Ask Eduardo Anglada). When I use this file then we get results but band gap in B1 phase is ~10eV which is quite far from

Re: [SIESTA-L] ANNOUNCE: LDA GGA pseudo databases

. Best, Eduardo On 12/03/2008, at 18:22, Eduardo Anglada wrote: Dear Users of Siesta, There is a new collection of pseudopotentials available for SIESTA! I have translated the LDA/GGA pseudos in the Fritz-Haber-Instute (FHI) format of ABINIT's database found in http://www.abinit.org/Psps

[SIESTA-L] Mailing list archives

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 use than the current version and it is english. The siesta team would like to thank the www.mail-archive.com for storing all the

Re: [SIESTA-L] Mailing list archives

On 02/04/2008, at 15:37, lan haiping wrote: should we subscribe to it again ? No, it is a copy of all the previous messages. Now it is easier to look for useful info, the search feature is much more useful. Eduardo Best On Wed, Apr 2, 2008 at 12:47 PM, Eduardo Anglada [EMAIL PROTECTED

Re: [SIESTA-L] Geometry Optimization

Hi, You should specify: MD.TypeOfRun CG (conjugate gradients relaxation) MD.NumCGSteps 100 (a maximum of 100 steps will be calculated. Of course if the forces are relaxed before the 100 steps are calculated then siesta will stop) The relavant section of the manual is:

Re: [SIESTA-L] regarding problem

Dear Sonia, It is discribed in: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/manual-2.0/node23.html Regards, Eduardo On 01/04/2008, at 13:21, Sonia Mehra wrote: der siesta users, Can anyone tell me that how to control the bandlines i.e. what type of changes can be

Re: [SIESTA-L] hello

Dear Sonia, There are several talks in: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/tutorials.html (you can find the talks and the exercises) which describe siesta basis sets. Also maybe you can post which is the element you are interested in. Regards, Eduardo On 28/03/2008,

Re: [SIESTA-L] ANNOUNCE: LDA GGA pseudo databases

it, but the number of 3d electrons in the Psf file was zero (3d 00.00). Is this a problem? Can I simply add 7 electrons to 3d orbital of the downloaded psf file? Thanks, Reza - Original Message From: Eduardo Anglada [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Tuesday, March 25, 2008 5:15

Re: [SIESTA-L] ANNOUNCE: LDA GGA pseudo databases

Dear Reza, Which one did you download? Best, Eduardo

Re: [SIESTA-L] Species not found error message - Parallel siesta.

Hi, Maybe the line with the number of spices is missing? post your input so we can take a look. Regards Eduardo On 15/03/2008, at 15:00, Kamaram Munira wrote: I have successfully run Siesta in serial mode till now. Recently, I am trying to run the parallel version and I get a error message

Re: [SIESTA-L] pseudo database; Zn configuration

Dear Andrei, On 13/03/2008, at 20:36, Andrei Postnikov wrote: Many thanks for Eduardo Anglada for uploading the ABINIT pseudos! Just two related questions: 1. Does somebody know whether there s a way to see from the .psf file if the core correction is included, and with which radius

[SIESTA-L] ANNOUNCE: LDA GGA pseudo databases

Dear Users of Siesta, There is a new collection of pseudopotentials available for SIESTA! I have translated the LDA/GGA pseudos in the Fritz-Haber-Instute (FHI) format of ABINIT's database found in http://www.abinit.org/Psps/?text=psps so now they can be used with SIESTA. The database can

Re: [SIESTA-L] Error in compiling( libfdf.a module could not be located, perhaps)

Hi, Your system lacks the basic development utils needed to build a library. Search the documentation and install them. Regards, Eduardo On 01/02/2008, at 12:58, vikas sharma wrote: I get the following error when run the make command in Src directory. (cd fdf ; make module) ar cru libfdf.a

Re: [SIESTA-L] Oxygen (triplet)

Hi Roberto, I think your only option is to use the DM.InitSpinAF and DM.InitSpin block. Take a look at the manual in: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ manual-2.0/node18.html#2854 Regards, Eduardo On 09/10/2007, at 22:03, Roberto Veiga wrote: Hi: I'm gonna do

Re: [SIESTA-L] How to visualize mesh points and potential on the mesh?

Dear Jingbin, The wsxm software reads directly any output of siesta. It's designed for the RHO and LDOS, but the format is the same for all the output of siesta, maybe you have to rename the other files. wsxm is free and can be found in: http://www.nanotec.es/ It only works in MS-windows.

Re: [SIESTA-L] How to calculate band-structure in SIESTA

Hi, Siesta is different and I think more powerful: you obtain the bands in a single run. The calculation is performed with the desired accuracy (you specify the k-sampling with the MonkhorstPack block or the kgrid_cutoff parameter) and at the end of the calculation if there is a BandLines

[SIESTA-L] How to define a ion?

Begin forwarded message: From: Eduardo Anglada [EMAIL PROTECTED] Date: 8 de octubre de 2007 11:16:41 GMT+02:00 To: Edgar Martinez Guerra [EMAIL PROTECTED] Subject: Re: [SIESTA-L] How to define a ion? Dear Egar, You should create a new pseudo. In the basis block you control the size

Re: [SIESTA-L] potential

Hi! remove the -L infront of the library path: ifort plrho.f -L/usr/X11R6/lib/libX11.a /share/apps/pgplot/ libpgplot.a -o plrho If the pglopt library was not compiled with ifort then you should include the other compiler libraries. Regards, Eduardo On 30/06/2007, at 8:51, Cherry Y. Yates

Re: [SIESTA-L] Symmetries

Dear Zoya, Siesta is designed for very large systems where, usually, the number of symmetries is very small, so it can't use them Regards, Eduardo On 13/06/2007, at 9:05, Zoya Shah wrote: Dear everyone I just have a question regarding symmetries. Is it possible to use the advantage of

Re: [SIESTA-L] parallel calculation with GGA method

Dear Helean, Try to increase the meshcutoff to something more reasonable: 100-150 Ry Regards, Eduardo On 02/06/2007, at 10:47, Mu J. Helien wrote: Dear Siesta users, I compiled the parallel version of siesta code sucessfully, but it seems that it can't run normally with GGA method. For the

Re: [SIESTA-L] How to set up these parameters in SIESTA

Dear C. H. Hu, The Prefactor could be around 150 and the Inner radious could be 3/4 of the cutoff radious. Regards, Eduardo On 14/05/2007, at 9:03, Chaohao Hu wrote: Dear Siesta users, How to set up the PrefactorSoft and InnerRadsoft inputing parameters when considering the new soft

Re: [SIESTA-L] pw vs. localized basis and pseudopotentials

This is José M. Soler answer to this question: Dear Nichols: The basis set and the pseudopotentials are completely independent things: - If you have no l=d pseudo projector, but you use l=d basis functions, they will feel only the local part of the pseudopotential, exactly like in a PW program

Re: [SIESTA-L] implementation question about MeshCutoff

Hi Nichols, The grid used for the calculation of the two center integrals (calculated in matel.f) is fixed to 2000Ry, while the one used for the three center integrals is set by the user using MeshCutoff. They are completely independent. My question is about SIESTA and how the MeshCutoff

Re: [SIESTA-L] Compilation error, How to start siesta programming

Dear Murali, Dear all, I have been trying to compile Siesta using f95 compiler and was not successful. Recently, i received help from one of the users to use g95 or gfortran compiler. As i used it, i could compile it successfully but when i started to run some programs that are

Re: [SIESTA-L] Geo-Optimization

Dear Neil, In order to optimize geometry you must use the variable MD.TypeOfRun CG The Zmatrix is a way (there are others) to provide the atomic positions. The relevant part of the siesta manual is: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ manual-2.0/node20.html Regards,

Re: [SIESTA-L] memory problem

Dear Saswata, I think you don't have enough free memory. Regards, Eduardo

Re: [SIESTA-L] Format of .XV file

Dear You Lin, Yes, they are bohr/fs. The XV uses the internal units of siesta: Ry, Bohr, fs. Regards, Eduardo On 08/03/2007, at 16:29, You Lin wrote: Hi, dear siesta developers: I'm trying to make change to .XV file. It looks like there's no document about its format. Then I made a

Re: [SIESTA-L] Molecular system

Dear You Lin, Siesta is really efficient treating empty space, so you should increase the vacuum size until there is no change in, for example, the total energy. Regards, Eduardo On 03/03/2007, at 19:44, You Lin wrote: Dear siesta collegues: My simulated system is molecular system with a

Re: [SIESTA-L] gen basis

On 06/03/2007, at 10:30, bipul rakshit wrote: hello siesta users, can any body tell me what is the exact way of using the gen basis programme. here i am sending the Sn.psf and Sn.fdf file I use the script as follows: i am in the directory of Sn sh ../gen-basis.sh Sn.fdf Sn.psf and then i got

Re: [SIESTA-L] Wavefunctions

Dear Nilolaos, The numerical atomic orbitals can be found in the ORB* files which siesta produces in the directory where it is run. The radial part of the orbitals (phi (r)) are stored as r, phi(r)/r**l where l is the quantum number of each one. The ORB* files are named following this

Re: [SIESTA-L] DSTEDC parameter number 8 - illegal value

Dear Lindsay, In which platform and which compiler are you using? Regards, Eduardo On 07/03/2007, at 16:36, Lindsay Shuller wrote: Dear Siesta users, I am new to the Siesta program and have compiled the version siesta2.0. I'm trying to do some test runs (following the manual), but I

Re: [SIESTA-L] radial and angular parts of basis functions

On 13/02/2007, at 3:22, Andrey V. Semichaevsky wrote: Hi Andrey, You're right, phiatm and rphiatm are the interface to the basis functions. Am I correct to say that phiatm.f is going to give me an implicitly angularly-dependent basis function if I call this function for various values

Re: [SIESTA-L] Segmentation fault for SIESTA version 2.0.1 MPI

On 09/02/2007, at 13:29, Rainer WILCKE wrote: Hello, Those tests aren't ment to be run in parallel, they are for the serial version. It's true that siesta should give an error message. Regards, Eduardo Hello, I am trying to create a MPI-version of SIESTA 2.0.1 at the ESRF for Claudio

Re: [SIESTA-L] Help: About gen-basis in siesta-2.0

Dear You Lin, Siesta reads the pseudopotential in semilocal form and computes the non-local projectors (Kleiman-Bylander), so if you specify use.basis true then siesta reads from the files all the information it needs. If you have just started using siesta I recommend the standard

Re: [SIESTA-L] Compilation :: Need Help

Hi, I attach an arch.make for the serial and parallel versions. Both of them use the intel compiler and cmkl. If you encounter any difficulties feel free to post them to the list. Regards, Eduardo arch.make-intel-opteron Description: Binary data arch.make-intel-opteron-parallel Description:

Re: [SIESTA-L]

On nov 15, 2006, at 12:57 PM, SuiYang wrote: Dear SuiYang, ¿Do you have the intel cluster math kernel library? ¿Do you have the intel mpi? If not ¿is it possible that you install them? If it is not possible to install them I will give you the detailed, step by step, instructions.

Re: [SIESTA-L] Au 6s pseudopotential

On nov 14, 2006, at 11:42 PM, Haiying He wrote: Dear Haiying, I don't have such a pseudo. My shortest convination of pseudo/basis set for gold is: %Block PAO.Basis Au 3 0.23116 n=6 0 2 E15.16639 3.56453 4.26384 1.58867 1.0 1.0 n=6 1 1 E

Re: Fwd: [SIESTA-L] about siesta-as-a-subroutine problem

Si en el fdf pones writexml (o un label equivalente, no me acuerdo) funcionara Edu Jose: Es algo que está ya en la lista de bug-fixes. Hasta que salga la 2.0.1 puedes arreglarlo a mano siguiendo las instrucciones que siguen. Saludos, Alberto Inicio del mensaje

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

On oct 27, 2006, at 3:58 PM, Marcos Verissimo Alves wrote: Hi Marcos, What you are describing are semicore states: several shells with the same l quantum number but different n quantum number. All of them share the same pseudopotential, but each resulting orbital is orthogonalized to those

Re: [SIESTA-L] any comment for NODAT

On oct 24, 2006, at 2:53 PM, 박준호 wrote: Hi, The NODAT preprocessor variable was used to configure the precision of several variables related to the paralelization. In SIESTA 2.0 is deprecated and can be removed from the arch.make. Regards, Eduardo. Hi, All In source code, there is a

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

Hi Derek, I haven't tried with lam-mpi, but with intel mpi there are problems if you link with a blacs compiled for mpi 1.2 while using mpi 2 (lam-mpi implements almost all of mpi 2). The problem is in one of the include files of the c interface of blacs, so it can be really difficult to detect

Re: [SIESTA-L] siesta compilation problem

Hi John, I attach an arch.make for sgi-altix. It uses the system blacs and scalapack optimized by sgi. Regards, Eduardo arch.make-sgi Description: Binary data On sep 26, 2006, at 1:46 AM, John B. Baba wrote: Hi all: Thanks lan and Marcos replay, I also try to compile siesta1.3

Re: [SIESTA-L] fundamental siesta parallel compilation question

On sep 6, 2006, at 7:07 PM, Marcel Mohr wrote: Hi Marcel, You should use the same compiler. If you change from one to another the compilation is going to be a nightmare. It is possible but really, really tricky. Regards, Eduardo Hello all I am trying to compile Siesta and required

Re: [SIESTA-L] Problem about compilering siesta

Dear Sir, There is a l_fce_pc_8.1* compiler. You can obtain a copy from your premier account at intel.com Regards, Eduardo On Wed, 2005-06-15 at 10:07 +0800, Mingsu Si wrote: Dear Sir, There is no l_fce_pc_8.1* compiler. In the web of Intel they say l_fc_pc_8.1* support em64t CPU.

Re: [SIESTA-L] Problem about compilering siesta

quotes and it probably it will compile successfully. Regards.- simingsu wrote: Dear Mr Eduardo Anglada I have just started to compile the SIESTA code with Intel ifort 8.1 compiler and MKL 7.2.1 libraries. The problem is that it is not able to compile atom.f file. The errors printed

Re: [SIESTA-L] Problem about compilering siesta

You don't provide too much info, in this kind of reports the operating system and cpu kind is really appreciated. The compiler is saying it doesn't understand the symbols format of the em64t lapack (mkl intel) library. Most probably you are compiling in another architecture. There are several

Re: [SIESTA-L] Implementation of MD in Siesta

Dear Benjamin, Siesta uses classical MD. In fact we have developed a new algorithm. If you are interested the reference is: http://dx.doi.org/10.1103/PhysRevE.68.055701 Efficient mixed-force first-principle molecular dynamics E. Anglada, J. Junquera and J. M. Soler, Phys. Rev. E *68*, 055701

Re: [SIESTA-L] polarized PAO !!

Dear Imad, The problem is in the 4 after Ga. It should be a 3 as you only provide 3 shells. The fourth (corresponding to the polarization orbital) will be added automatically by siesta. Regards, Eduardo %block PAO.Basis Ga 3 n=3 2 2 0.00 0.00 n=4 0 2

  1   2   >