Re: [SIESTA-L] Issues with building and compiling new siesta

You compiler (gnu 4.8.5) is *very* old. Please upgrade to a modern version. Best regards, Alberto - El 6 de Junio de 2024, a las 19:09, Boubacar Traore escribió: | I finally sorted out the issue of scalapack linking by adding its path to | LIBRARY_PATH instead of LD_LIBRARY_PATH

Re: [SIESTA-L] Passing constraint harmonic energy through constr.f

ink to the hydrogen one, e.g. H.psf. I hope this helps. Alberto - El 16 de Noviembre de 2023, a las 04:17, Francisco Garcia escribió: | Dear Prof. Garcia | Many thanks for your response. | I looked up the MM.Potentials block but I couldn't figure out how to apply the | harmon

Re: [SIESTA-L] Passing constraint harmonic energy through constr.f

a harmonic potential. Best regards, Alberto - El 11 de Noviembre de 2023, a las 09:13, Francisco Garcia escribió: Dear Users, The constraint subroutine takes the form: subroutine constr( cell, na, isa, amass, xa, stress, fa, ntcon ). It doesn't contain information about energy.

Re: [SIESTA-L] Siesta fatbands / building utilities in 5.0

_build stands for the CMake build directory and for the appropriate subdirectory in the Util hierarchy. The build_all.sh script is a fossil we forgot to remove… If you used an old version of ‘fat’, the format of the HSX file might have changed. Please use the latest version. Alberto

Re: [SIESTA-L] Error in compiling siesta-master (28 Sep. 2023)

d building steps. Thank you for your feedback. Alberto - El 28 de Septiembre de 2023, a las 21:33, Reza Behjatmanesh-Ardakani escribió: | Hi | I used following command for compiling siesta-master: | | cmake -S. -B_bui

Re: [SIESTA-L] About Work Function Calculation on Au

to check that you reach a flat region in the vacuum. Alberto - El 15 de Marzo de 2023, a las 11:41, yh46 escribió: | Hello Dear SIESTA Users, | I am trying to do a work function calculation of Au 111 surface. The | work function I get if 3.5 eV, which is quite different from | experimenta

Re: [SIESTA-L] Specify file path for pseudos?

Hi, This is something that we are planning to implement. For now, if file space is a problem, you could use symbolic links from a central location to each execution directory. Best regards, Alberto - El 3 de Feb de 2023, a las 19:33, Daniel Bennett escribió: | Hi all, | I was

Re:[SIESTA-L]

Hi, For some reason, you are using commas (",") instead of dots (".") as decimal separators. In fortran, a comma in an input line separates items. This confuses the program. You should check your 'locale' settings. Alberto - El 7 de Noviembre de

Re: [SIESTA-L] (Wrong block specification)

Hi, You should remove the comment character from: #%endblock LatticeVectors Alberto - El 21 de Septiembre de 2022, a las 12:23, Amal Yassin escribió: | Dear Siesta Users | I make run to carbone nanotube armchair, but i find an error, can anyone helle | me to solve this error? ( I

Re: [SIESTA-L] (problems with polarization orbital when using Mg.psml)

Dear Rajesh, I quote from (the source of) the Siesta manual: \item The default perturbative scheme for polarization orbitals can fail in very specific cases. When the polarization orbital has to have a node due to the presence of a lower-lying orbital with the same $l$, the program can (if e

Re: [SIESTA-L] Question on VCA approach

ra conditions on the pseudopotential of the alchemical species. Best regards, Alberto - El 28 de Junio de 2022, a las 14:09, RCP pasia...@cnea.gov.ar escribió: | Dear developers, | | I'd like to know if there is a specific reference for the method | of mixing pseudopotentials implemented

Re: [SIESTA-L] Installing Siesta GPU acclerated version

if [ $rank -lt $limit0 ] then export CUDA_VISIBLE_DEVICES=0 elif [ $rank -lt $limit1 ] then export CUDA_VISIBLE_DEVICES=1 elif [ $rank -lt $limit2 ] then export CUDA_VISIBLE_DEVICES=2 else export CUDA_VISIBLE_DEVICES=3 fi $@ I

Re: [SIESTA-L] [SPAM] Siesta parallel version installation on HPC

Hello, You seem to be missing the BLAS library in your link statement. It could be as simple as adding -lblas to your link line, but it would depend on your installation. Best regards, Alberto - El 22 de Junio de 2022, a las 23:14, Ghazanfari, Sarah sarah.ghazanf...@ndsu.edu escribió

Re: [SIESTA-L] << two set of charge calculations >>

setup. Radii (standard, H): 1.000 0.600 dhscf: Vacuum level (max, mean) =0.636991 -0.068255 eV cite: Please see "h2o.bib" for an exhaustive BiBTeX file. [...] in which one gets two blocks, one for Voronoi and another one for Hirshfeld populations. Alberto - El 14 de Jun

Re: [SIESTA-L] Error for perturbative polarization for Li atom

Hi, As the error message suggests, you can try the non-perturbative options (see manual). I hope this helps. Regards, Alberto - El 13 de Junio de 2022, a las 12:22, Reza Behjatmanesh-Ardakani reza.b@gmail.com escribió: | Hi, | I used following fdf file for Li unit cell

Re: [SIESTA-L] Charge in occupied basis is different from valence charge

-tune the automatic split-valence options. I hope this helps. Alberto - El 27 de Mayo de 2022, a las 00:01, Andres Tellez Mora at00...@mix.wvu.edu escribió: | Dear SIESTA users. | | I am trying to run a calculation with a SmNiO3 structure. I am using the pseudo | potentials from the

Re: [SIESTA-L] Forces on crystalline atoms are not zero

Hi, There must be some issue with your input. Could you share it? Regards, Alberto - El 28 de Marzo de 2022, a las 02:52, Francisco Garcia garcia.ff@gmail.com escribió: | Dear Users | | I performed a series of single point energy calculations on an FCC crystal by | varying the

Re: [SIESTA-L] Using prior calculation for spin-orbit calculation

Hi Francisco, You need to run a new (SOC) calculation, but you can re-use the DM file (density matrix) from the previous run to initialize the SOC calculation, thus typically reducing the number of steps needed for convergence. Regards, Alberto - El 27 de Marzo de 2022, a las 09:34

Re: [SIESTA-L] [***RedIris: Posible SPAM***] [***RedIris: Posible SPAM***] Output units in the *.bands file

Hi, The units are indeed Bohr^-1. But in the .bands file (assuming you are using the 'bandlines' option), what is printed is the cumulative path length in reciprocal space. I hope this helps. Alberto - El 10 de Feb de 2022, a las 04:39, Pasan Henadeera henadeer...@gmail.com

Re: [SIESTA-L] Fully Relativistic Psuedopotential for SIESTA

relatively straightforward, with basic help in the page: https://gitlab.com/siesta-project/siesta/-/wikis/How-to-build-the-master-version-of-Siesta We are planning a beta release of Siesta 5.X in the next few weeks. Best regards, Alberto - El 6 de Feb de 2022, a las 08:50, Daniel

Re: [SIESTA-L] Error interpretation:Total charge in occupied basis states different from valence charge

Hi, You have a number of errors in your input file: -- The atomic number of C is 6, not 12 -- For C and N, the d orbital should have n=3 -- For H the p orbital should have n=2 I hope this helps. You must have made changes to Simune's files... Alberto - El 2 de Feb de 2022, a las

Re: [SIESTA-L] How to compile the psml-support branch with PEXSI

Hi, As explained in https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions you need to use the rel-MaX-1 branch, which contains both PSML support and the ELSI interface. Best regards, Alberto - El 17 de Ene de 2022, a las 02:50, Chong Wang ch-w...@outlook.com

Re: [SIESTA-L] forcesToMaster: Etot or free energy?

t what is sent through the interface. What do other codes send through the interface? Best regards, Alberto [1] Kresse, G., and J. Furthmüller. 1996. “Efficiency of Ab-Initio Total Energy Calculations for Metals and Semiconductors Using a Plane-Wave Basis Set.” Computational Materials Science

Re: [SIESTA-L] Device Relaxation malfunction

at the end of the page: https://docs.siesta-project.org/projects/siesta/tutorials/basic/structure-optimization/index.html Alberto - El 5 de Octubre de 2021, a las 14:54, Ziba Torkashvand zi.torkashv...@gmail.com escribió: | Dear all siesta users, | I'm trying to relax my structure

Re: [SIESTA-L] problem with projected band in SIESTA

-Siesta-versions I hope this helps. Alberto - El 17 de Septiembre de 2021, a las 13:44, alokkarn0 alokka...@gmail.com escribió: | I tried so many times in the SIESTA_psml version, I don't know where I did make | mistakes, that every time "file.bands.WFSX" did not work for a p

Re: [SIESTA-L] Compiling siesta 4.1.b4 and 4.1.5 with intel tools fails at iogrid_netcdf.F90

use 'make'. Alberto - El 12 de Jul de 2021, a las 09:32, Jimenez Alfaro, Jorge (NASERTIC) jjime...@nasertic.es escribió: | Hello, | | Any help will be really appreciated. Many thanks in advance | | I have modified line 33 of Makefile regarding a recipe that used to work for |

Re: [SIESTA-L] How to get the numerical value of electron density

e function are written to standard output. c Other information is written to standard error. Best regards, Alberto - El 13 de Junio de 2021, a las 19:54, Jyotirmoy Deb deb.jyotirmo...@gmail.com escribió: | I want to get the numerical value of electron density rho (x,y,z) along X, Y,

Re: [SIESTA-L] constr.f problems

Hi, For this simple kind of constraint, you should not need to write your own constr.f file. You can use the constraint-specification options described in the manual. Best regards, Alberto - El 20 de Mayo de 2021, a las 10:40, Pablo Álvarez Rodríguez pablo96carnic...@gmail.com

Re: [SIESTA-L] Finding fat bands without redoing the calculation

option dm-use-save-dm. Alberto - El 31 de Marzo de 2021, a las 18:56, El-abed Haidar ehai2...@uni.sydney.edu.au escribió: | Good evening, | |1. I was wondering for a large SIESTA calculation, if I forgot the commands in |the fdf file to do a fat band calculation and do not want to

Re: [SIESTA-L] Passivation with hydrogen

do-H atoms. You could use directly the 'atom' program, or use the utilities in Util/VCA to generate pseudos for "fractionally-charged" H atoms. Alberto - El 22 de Feb de 2021, a las 17:02, Mochena, Mogus D. mogus.moch...@famu.edu escribió: | Dear siesta users: |

[SIESTA-L] Fwd: [CCC-UAM #1102] Resolved: Re: << Compiling Utils using build_all scrip >>

Hola, Soy co-administrador de la lista 'siesta-l' que usa el servidor de listas 'sympa' de la UAM. Desde hace unos días, aparecen en la lista mensajes como el que sigue a continuación. Saben qué puede estar pasando? Muchas gracias. Saludos, Alberto García ICMAB-C

Re: [SIESTA-L] << Compiling Utils using build_all scrip >>

Hi, You do not give details, but you must be using a very old version... Try downloading a new one from the psml-support branch in Gitlab. I hope this helps, Alberto - El 3 de Feb de 2021, a las 15:30, I. Camps ica...@gmail.com escribió: | Hello SIESTers, | | I am trying to compile

Re: [SIESTA-L] SIESTA (GitLab version) installation failure

Hi, Since you are using a recent 'master' version, you might want to look into the Obj/ARCH-EXPERIMENTAL directory. There you will find a more structured way of organizing the building. Alberto - El 16 de Dic de 2020, a las 10:15, Tamas Karpati tkarp...@gmail.com escri

Re: [SIESTA-L] Issue with Denchar

(WFSX) file. Alberto - El 16 de Dic de 2020, a las 04:19, El-abed Haidar ehai2...@uni.sydney.edu.au escribió: | I will have to agree with Alberto because other systems worked when i did not | specify the energy levels. | My question then is when i used | WFS.Energy.Min -5 eV

Re: [SIESTA-L] Issue with Denchar

In the absence of more information (you might want to enable debugging symbols to see where the error occurs): - It might be that the energy range you specified does not contain any wavefunctions (the program should anyway not crash... You might check this with the Util/WFS/readwfx program).

[SIESTA-L] MaX Siesta webinar -- Sept 22 @3pm CEST

in: http://max-centre.eu/webinar/new-developments-siesta-high-performance-materials-simulations Information on past and future MaX webinars can be found in: http://max-centre.eu/webinar/ Best regards, Alberto Garcia for the Siesta developers -- SIESTA is supported by the Spanish

[SIESTA-L] Fw: How to read WFSX file

of Siesta (including the latest along the rel-4.1 branch in Gitlab) have an updated Util/readwfx utility with more options and a simpler interface. Alberto - El 4 de Jul de 2020, a las 20:02, Medondjio Linda lindamedond...@yahoo.fr escribió: | Dear Siesta user, | | I would like to

Re: [SIESTA-L] wave function coefficientes in a calculation with SO

overview of the Siesta versions available, and where to find them, please see: [ https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions | https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions ] Best regards, Alberto - El 6 de Mayo de 2020, a las 11

Re: [SIESTA-L] wave function coefficientes in a calculation with SO

/tree/master Best regards, Alberto - El 3 de Mayo de 2020, a las 11:12, Pablo Aguado escribió: | Hi everyone, | The writing of the WFSX file is not currently implemented in the case of a | calculation including spin-orbit. Is there any other straightforward way to | extract the wave

Re: [SIESTA-L] Forces are 0.000000 on all atoms in an polymorph of BiFeO3 crystal

Dear Dr. Popov, Your unit cell is cubic, and the coordinates show a highly symmetric pattern. If your atoms happen to be in centrosymmetric positions, the forces must be zero. - El 26 de Feb de 2020, a las 19:14, popov po...@ipb.ac.rs escribió: | Dear Siesta users, | | I have got all for

Re: [SIESTA-L] Negative translation acoustic modes in phonon band structure

bookeeping artifact, and will not "fold" your phonon band structure. That is a concept that only applies to electronic band structures. So please do use a supercell... Alberto - El 4 de Dic de 2019, a las 22:11, popov po...@ipb.ac.rs escribió: | Hi, | | My Siesta calcula

Re: [SIESTA-L] dft-d3 model (dispersion correction)

Dear Azadeh, No, the current Grimme-D method in Siesta is the one using only two-body potentials. See: J Comput Chem 25: 1463–1473, 2004 and J Comput Chem 27: 1787–1799, 2006. Alberto - El 22 de Septiembre de 2019, a las 07:34, Azadeh Ayatollahie azadeh.ayatolla...@gmail.com escribió

Re: [SIESTA-L] compiling the PSML-compatible version

PI-enabled version of libGridXC. Alberto - El 7 de Junio de 2019, a las 16:29, Pablo Aguado pagu...@gmail.com escribió: | Hi everyone, | I'm trying to compile the PSML-compatible version of siesta, but I get the | error: | | siesta_init.F(397): error #6631: A non-optional actual argument mu

Re: [SIESTA-L] Folding of H and S is implicitly performed

of COOP/COHP curves, for example), will not work properly if the matrix elements of S and H have been "folded". In this case you can use the 'ForceAuxCell' option (see the manual). Alberto - El 27 de Feb de 2019, a las 04:15, Mina Sedighi msedi...@uwaterloo.ca escr

Re: [SIESTA-L] Overflow in registry

forthcoming version the pool will be made dynamically resizable. Best regards, Alberto > On 12 Feb 2019, at 11:57, Alejandro Martín wrote: > > Dear siesta users, > > I am struggling with a "Overflow in registry" message in siesta/4.1-b3 > version > when I try to ru

Re: [SIESTA-L] MPI compilation of trunk version (Linux x86/64)

Hi, You are using the C++ compiler ('g++') instead of 'gcc' (C compiler). This causes some extra name mangling in 'sockets.o' that confuses the linking stage. Best regards, Alberto - El 20 de Noviembre de 2018, a las 04:30, Zhiping Xu x...@tsinghua.ed

Re: [SIESTA-L] parallel version issue of 4-1.-b3, m_orderbands.o: undefined reference to `indxg2p_'

/blacsCinit_MPI-ppc64-0.a /apps/scalapack/64/lib/blacs_MPI-ppc64-0.a -L/apps/scalapack/64/lib -lscalapack Alberto - El 22 de Septiembre de 2018, a las 22:00, SPT saravp...@googlemail.com escribió: | Hi | | Issue is : siesta 4.1-b3 MPI" Installation. I found the following issue and |

Re: [SIESTA-L] molecular dynamics (AIMD) calculations

Dear Saif, There is no difference, really. You compute the forces with ab-initio methods, and evolve the ions using Newton's equations with those forces. You had bad luck with the referee. Alberto - El 10 de Jul 2018, a las 23:46, sullah sul...@fisica.ufjf.br escribió: | Dear Al

Re: [SIESTA-L] molecular dynamics (AIMD) calculations

To clarify, what Siesta and all the other mentioned packages do is really “ab-initio molecular dynamics”, as opposed to “molecular dynamics with classical or effective potentials”. Alberto > On 3 Jul 2018, at 01:24, sullah wrote: > > Dear Najmeh. > > In SIESTA, you ca

Re: [SIESTA-L] [SUSPECTED][RI] In Spin orbit calculation, can I read *.ion file as a pseudopotential?

Hi, This is because the .ion file only contains the PAOs and the “scalar” KB projectors. The extra information in the .psf file (SO-part of the semilocal pseudopotentials) is needed to build the spin-orbit contribution to the Hamiltonian. Best regards, Alberto > On 15 Mar 2018, at 02

Re: [SIESTA-L] asterisks and NAN in output

Siesta is quite efficient. For very large systems, if you have access to a large computer, the PEXSI method (available in version 4.1-b3) might be suitable. Or you might want to try the new O(N) CheSS solver, available in the trunk version in Launchpad. Best regards, Alberto > On 25

Re: [SIESTA-L] Restart without scf loop

lack of SCF convergence, but it would be harmless (assuming that you are using the correct DM…) I hope this helps. Alberto > On 24 Jul 2017, at 04:28, Nicolas Duchêne wrote: > > Hi all, > > I was wondering if there was a way to restart a “calculation” without >

Re: [SIESTA-L] Segmentation fault in parallel run for molecule type system

, whereas your mesh-cutoff might be on the small side. Best regards, Alberto > On 11 May 2017, at 00:59, nicolas.duch...@polymtl.ca wrote: > > Greetings SIESTA users, > > I’m a new user, and have made attempts at modelling a silver nanocluster of > 13 atoms (ic

Re: [SIESTA-L] Problems compiling DENCHAR

Hi Ian, Please make sure that you are using GNU make. We use the VPATH feature to find source files in other directories. Also, try to do a “make clean” in case there is some previous corruption. Best regards, Alberto > On 24 Apr 2017, at 13:46, Ian Shuttleworth wrote: > >

Re: [SIESTA-L] Ca basis sets and pseudo potentials for systems containing Ca and O

, Alberto > On 2 Mar 2017, at 10:35, Mark Iron wrote: > > Dear all, > > I need to run some calculations for CaCO3 crystals. Because of the nature of > the problem (I need the vibrational frequencies of large unit cells) I need > an order(N) method, which is available in

Re: [SIESTA-L] NETCDF error

Hi, In your arch.make, replace -DNCDF by -DCDF, type “make clean” and “make”. Alberto > On 30 Jan 2017, at 11:33, RAJAN SINGH wrote: > > Dear Siesta users > > I am facing following errors while trying to install 4.1-b1 in parallel mode > with NETCDF: > > Fatal

Re: [SIESTA-L] Continuation Run

to preserve the coordinates, use the SystemLabel.STRUCT_OUT file, renaming it to SystemLabel.STRUCT_IN, and use the option Use.Struct.File T Alberto > On 27 Jan 2017, at 02:25, Seyed Mohammad Tabatabaei wrote: > > Dear all, > > I have a converged .DM file from a previous c

Re: [SIESTA-L] empty denchar files

The files are of the form SystemLabel.Extension. In your case, input-ok-og.DIM, etc. Alberto On 24 Oct 2016, at 08:14, Marco Fronzi wrote: > Dear Siesta Users, > > I am trying to plot charge density and wavefunction using denchar. > In the working directory I put the followin

Re: [SIESTA-L] << error compiling siesta-4.1-b1 in m_mixing.F90 >>

Hi, Indeed, the CONTIGUOUS keyword is a F2008 feature, not implemented yet in all compilers. For now you can apply the patch attached to https://bugs.launchpad.net/siesta/+bug/1619437 to fix this problem, or simply delete the CONTIGUOUS keyword. Best regards, Alberto On 14 Sep 2016

Re: [SIESTA-L] to bug or not to bug!

at the file Src/Sys/DOCUMENTED-TEMPLATE.make and at other examples in Src/Sys. You have probably done that to find out about FC_SERIAL. Best regards, Alberto On 14 Sep 2016, at 09:00, Mersad Mostaghimi wrote: > > Dear developers, > In compiling siesta-4.0.0 with mpiifort there i

[SIESTA-L] Bug fix for MRRR switch-off option (Re: Compilation error of Siesta 4.1(b1))

Hi, Thank you for the report. There is indeed a bug in the implementation of the -DSIESTA__NO_MRRR option. A patch is available. See: https://bugs.launchpad.net/siesta/+bug/1622526 Regards, Alberto On 09 Sep 2016, at 17:03, Jariyanee Prasongkit wrote: > Dear Siesta team, >

Re: [SIESTA-L] problem with gnubands

in the BZ, which is not appropriate for a band structure plot. It is perhaps unfortunate that the file extension is the same for both cases. We make a note to change it. Regards, Alberto On 09 Sep 2016, at 12:27, Uttam Paliwal wrote: > hi > I am using siesta-4.1-b1 and running the

[SIESTA-L] Release of Siesta-4.0

We are pleased to announce the release of Siesta-4.0. This version should be the default choice for production for most users. You can read the Release Notes and obtain the tarball in the release page: http://launchpad.net/siesta/4.0/4.0 Note in particular the BACKWARD COMPATIBILITY ISSUES an

Re: [SIESTA-L] Siesta to be released with GPL license

beta very soon. Best regards, Alberto, for the Siesta developers. On 20 May 2016, at 16:51, Grigory Shamov wrote: > Dear Alberto, > > Is this retroactive? I.e., do we still protect older SIESTA versions, > asking users to agree to the old Academic access licenses? > > --

Re: [SIESTA-L] Siesta to be released with GPL license

Dear Grigory, That is good question... and I am not sure yet what the best answer is. We are having a developers meeting at the end of the week. I will raise the issue then and will let you know. Best regards, Alberto On 20 May 2016, at 16:51, Grigory Shamov wrote: > Dear Albe

Re: [SIESTA-L] discrepancy in kpoints generation for band structure calculation

-structure calculation in the same run. Since the k-point coordinates for the band-structure calculation are computed at the beginning of the run, they would be appropriate for the initial cell, not the final one. This can be considered a bug or a feature... Alberto On 19 May 2016, at 03:13, Zhang

Re: [SIESTA-L] discrepancy in kpoints generation for band structure calculation

-relaxation run, as the k-points would be appropriate for the original cell. Regards, Alberto On 18 May 2016, at 12:18, Zhang Aihua wrote: > Dear All, > > I have noticed that if I do a single-point band structure calculation with > > UseStructFile true > > and simul

[SIESTA-L] Siesta to be released with GPL license

The SIESTA developers have decided to change the licensing conditions for the code. From now on, SIESTA will be released under the GPL open-source license (https://en.wikipedia.org/wiki/GNU_General_Public_License). In the past SIESTA had always been free for academic use, but re-distribution w

Re: [SIESTA-L] error while siesta-4.0b-485 installation....

budget is tight you can get the free Gfortran compiler. Alberto On 06 Apr 2016, at 09:33, Nick Papior wrote: > Please try and update your compiler. > You should use a 2003 compliant compiler. > > 2016-04-06 7:30 GMT+02:00 Suman deep : >> sir, >> i m getting the following

Re: [SIESTA-L] CHARGE DENSITY PLOT USING DENCHAR

format, using the tools in Util. As of now there is no direct output of the "partial density matrix" in an energy-window, so Denchar (which need a DM) cannot be used. If you are interested you could modify the code yourself to insert a call to the routine that outputs density matrices

[SIESTA-L] A note of warning regarding pseudopotentials for vdW-DFT calculations

by that of the vdW functional to be used. This note will be added to the Siesta documentation as soon as possible. Best regards, Alberto On 17 Feb 2016, at 00:56, I. Camps wrote: > Hello Ticu, > > You have to generate your own vdW-DFT pseudos. > > What I did: > - Downlo

Re: [SIESTA-L] Spin-orbit interaction

Hi, The spin-orbit interaction is not yet included in the released version of Siesta. It will be in the next few months. Regards, Alberto On 10 Feb 2016, at 09:32, Abdullahi Lawal wrote: > Dear Siesta user. > Please some body should help me, i want to calculate the stru

Re: [SIESTA-L] Installation of Siesta-trunk-462

newer siesta-4.0b version. There is no point in using trunk-462. You should download siesta-4.0b. Alberto On 08 Feb 2016, at 10:33, RAJAN SINGH wrote: > Actually I am getting same errors as one person face when installing Siesta > 4.0 version. (http://www.mail-archive.com/siesta-l%40

Re: [SIESTA-L] [POSSIBLE SPAM][R] Compilation problems

Hi, 1. Please copy Src/Sys/nolibs.make to Obj/arch.make. 2. Change the name of your compiler if needed in arch.make. 3. In Obj, type "make clean" and then "make" Regards, Alberto On 04 Feb 2016, at 10:50, Zaw Myo Win wrote: > Dear Alberto, >

Re: [SIESTA-L] Compilation problems

If you are not using an external lapack+blas library, you should use COMP_LIBS=linalg.a in the arch.make file to compile all the linear-algebra code in Src/Libs. Version 4.0 needs extra code that is not in the file Src/Libs/lapack.f. See Src/Sys/nolibs.make. Regards, Alberto On 04

Re: [SIESTA-L] CHARGE DENSITY 3D PLOT

Please see the "Local Density of States" section of the manual. On 30 Jan 2016, at 11:35, Anju Saroha wrote: > Hi to all, > > I am having a doubt in plotting charge density in 3D mode. I tried using > DENCHAR utility program. I want to know how one can plot charge density in > some specific e

Re: [SIESTA-L] grid2cube

Dear Jin, The 'STRUCT' file must be in a special format produced by Siesta. Every run produces by default a .STRUCT_OUT file. This is the one you need to use. The xyz format is not supported by g2c_ng. Alberto On 02 Jan 2016, at 03:08, Jingxian Yu wrote: > Dear Alberto

Re: [SIESTA-L] grid2cube

Hi, In the new version siesta-4.0b available at the Siesta website there is an updated grid2cube (named g2c_ng) in the Util/Grid directory that can handle non-orthorhombic cells. Regards, Alberto On 31 Dec 2015, at 11:20, Nick Papior wrote: > I have created a small utility in pyt

[SIESTA-L] Announcement: Beta version of Siesta-4.0 available

We are happy to announce the availability of a beta version of the upcoming Siesta 4.0 release. This version includes the van der Waals functionals, the new load-balancing code for real-space grid operations, a Wannier90 interface, a new Orbital-Minimization-Method solver, and other improvements a

[SIESTA-L] Guidelines for mailing list etiquette -- periodic posting

This is a semi-automatic periodic posting to the Siesta mailing list. The mailing list can be a good resource for everybody, provided that we can abide by a few common-sense guidelines: * Before posting, make sure that you have made a fair effort at learning about the issue in the documentatio

Re: [SIESTA-L] can not have band structure with gnubands??

Hi, You want the 'prefix.bands' file. The .BONDS file contains bond-length information... By the way, if you use the 'pi/a' option for the k-point scale, make sure that you have a LatticeConstant XX.XX line in your input file. Regards, Alberto On 16 Jul 20

Re: [SIESTA-L] FoX: Compile with FC or FC_SERIAL?

Hi Mike, The FoX library does not contain any MPI calls, so it does not need mpif90 for compilation. However, if you link it with a code (such as Siesta) with MPI calls, then you do need to link it with mpif90. Regards, Alberto On 11 Jul 2014, at 22:10, Michael R. C. Williams wrote

Re: [SIESTA-L] Version mismatch of documentation and source code

version, the manual found under the "Documentation" hierarchy of pages might not be in sync with the latest released snapshot. These manuals are provided for the convenience of quick lookup of standard options. Best regards, Alberto On 08 Jul 2014, at 21:08, Michael R. C. Willia

[SIESTA-L] Siesta Tutorial in Zaragoza: a few slots still available

(e.artacho _at_ nanogune.edu) Alberto Garcia, Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC) (albertog _at_ icmab.es) * Instructors: Jose Soler, Universidad Autonoma de Madrid Georg Huhs, Barcelona Supercomputing Center Javier Junquera, Universidad de Cantabria Emilio Artacho, CIC

[SIESTA-L] Announcement: SIESTA Tutorial, Zaragoza, June 16-19 2014

Organizers: Emilio Artacho, CIC NanoGUNE Consolider, Donostia-San Sebastian (e.artacho _at_ nanogune.edu) Alberto García, Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC) (albertog _at_ icmab.es) * Instructors: Jose Soler, Universidad Autonoma de Madrid Georg Huhs, Barcelona Supercomput

Re: [SIESTA-L] How to run BSSE corrections with synthetic atoms?

the fix to the development version will follow soon. My apologies to Alexander Vozny for missing his earlier report about the problem. Best regards, Alberto

Re: [SIESTA-L] << Generating pseudopotential with semi-core states for Pb >>

d10 they are not adequate. But do you really need the spin polarization? Note that the original source you quote used a relativistic pseudo, which is the standard practice, even for calculations in which you are later going to consider spin. Regards, Alberto On Nov 28, 2013, at 7:33 PM, I

Re: [SIESTA-L] Atomic charges

Hi Herbert, Siesta is also able (as of 3.2) to do Hirshfeld and Voronoi charge partitioning analyses. Alberto On Thu, Jun 20, 2013 at 3:21 PM, Herbert Fruchtl < herbert.fruc...@st-andrews.ac.uk> wrote: > Just to add to the discussion that started with the question about PDOS >

Re: [SIESTA-L] PDOS: Is there a way to specify radius of projection?

Hi Benedikt, SIESTA does not need projections, as the basis orbitals are localized on the atoms. You get naturally the "chemical" information one is used to. Plane-wave codes such as vasp do need projections to get some kind of "local" information from the delocalized basis.

Re: [SIESTA-L] can't scale to 128 procs

better than what you get with 3.X. If you spend a significant fraction of the CPU time of your runs in dhscf, this will make a difference. If not, you could increase the mesh cutoff or the size of your box to be able to use more processors for the diagonalization part. Best regards, Alberto

[SIESTA-L] New Siesta development snapshot (trunk-433)

We have released a new Siesta development snapshot (trunk-433) which includes: - The implementation (by Fabiano Corsetti) of an orbital-minimization method without localization that can be used as an alternative to diagonalization. - The JobList suite of utilities (by Jose Soler) to organize,

[SIESTA-L] Release of Siesta-3.2

We are happy to announce the release of Siesta 3.2. Users are encouraged to use this version for production runs. You can find the Siesta 3.2 release in the "Access to the code" section of the Siesta website. To report any remaining issues, see Docs/REPORTING_BUGS Thanks for your patience and c

[SIESTA-L] New development version snapshot

Dear Siesta users, We have corrected several bugs and inconsistencies in the development version, and released a new snapshot (trunk-427). Some of the improvements affect the new TranSiesta and TBTrans code contributed recently by Nick Papior Andersen, of the Technical Univ. of Denkmark. The

Re: Re: Re: [SIESTA-L] post-processing the energy band

Liu, You should upgrade to the latest versions, both along the 3.X branch and the development ("trunk") branch. Alberto On Thu, Nov 8, 2012 at 7:42 AM, liuyunlong0902 wrote: > Thanks for your suggestion. Here I include the input and output file, which > is just an example

Re: [SIESTA-L] Enhancements to the TranSiesta/TBTrans code

NETCDF_INCLUDE seems to be a fossil used by the old configure mechanism. Please see Src/Sys/DOCUMENTED-TEMPLATE.make for a full explanation of the variables used. Best regards, Alberto On Wed, Oct 31, 2012 at 5:42 PM, Guangping Zhang wrote: > Dear users and developers: > > I have encout

[SIESTA-L] Enhancements to the TranSiesta/TBTrans code

things to watch out for and explore in the new version. To report any remaining issues, see Docs/REPORTING_BUGS Thanks for your patience and continuous support. The Siesta team October 31, 2012 Dr. Alberto Garcia -- Email: alber...@icmab.es Institut de Ciencia de Materials de Barcelona - C

[SIESTA-L] Code updates on the Siesta website: siesta-3.1-pl18, siesta-trunk-421

fixes. We would be grateful for any bug reports. Please follow the guidelines in the Docs/REPORTING_BUGS file. Regards, Alberto Dr. Alberto Garcia -- Email: alber...@icmab.es Institut de Ciencia de Materials de Barcelona - CSIC Campus de la UAB, E-08193 Bellaterra, SPAIN Tel: +34-93

Re: [SIESTA-L] about psp gen using ATOM

Hi Bing, This is a cosmetic bug that only affects the creation of the optional XML file. The psf file would still be correct. The bug has been fixed in siesta-3.1-pl18, available on the Siesta website. Alberto On Oct 12, 2012, at 4:01 AM, Huang Bing wrote: > Hi, siesta users > >

Re: [SIESTA-L] Help with new Hirshfeld population code

Hi, Brad, Please try the updated version (siesta-3.1-pl11) from the Siesta website. Best regards, Alberto On Sat, Oct 6, 2012 at 6:32 AM, Brad Wells wrote: > Hi Siesta Users, > > I am interested in using the new Hirshfeld code for calculating partial > charges, as th

[SIESTA-L] New development snapshot

Dear Siesta users, A new development snapshot (siesta-trunk-408.tgz) is available for download by eligible users at the Siesta website. This snapshot contains the latest bugfixes, and is a step closer to a beta-relase that will include the new functionality we have been working on since the 3.0

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